Tree seedling establishment under insect herbivory: edge effects and inter- annual variation

As the density and species composition of insects may change in relation to distance from the forest edge, the role of herbivory in tree establishment may also change across edges. To determine the importance of insect herbivory in tree establishment, insect densities were experimentally altered at different distances from the forest edge. Plots were established at three distances from the edge, with plots located in forest, edge, and field habitats. In half of each plot, insect densities were reduced by insecticide application. Seeds of two tree species, Acer rubrum and Fraxinus americana, were planted into each plot in 1995. The experiment was repeated in 1996 with the addition of Quercus palustris and Quercus rubra.Distance from the forest edge was the most important factor in determining seedling emergence and mortality. Overall seedling performance increased from field to edge to woods, although responses varied among species. In 1995, a drought year, insect removal increased emergence and decreased mortality of tree seedlings. In 1996, a year with normal precipitation, insect removal had much less effect on A. rubrum and F. americana. For the two Quercus species, mortality was reduced by insect removal. The tree species differed in their susceptibility to insect herbivory, with Acer rubrum the most susceptible and Fraxinus americana the least. Herbivory by insects was shown to have the potential to affect both the composition and spatial pattern of tree invasions. Herbivore importance differed greatly between the two years of the study, making the interaction between insects and tree seedlings variable both in space and time.     

The UvrD303 Hyper-helicase Exhibits Increased Processivity

DNA helicases use energy derived from nucleoside 5′-triphosphate hydrolysis to catalyze the separation of double-stranded DNA into single-stranded intermediates for replication, recombination, and repair. Escherichia coli helicase II (UvrD) functions in methyl-directed mismatch repair, nucleotide excision repair, and homologous recombination. A previously discovered 2-amino acid substitution of residues 403 and 404 (both Asp → Ala) in the 2B subdomain of UvrD (uvrD303) confers an antimutator and UV-sensitive phenotype on cells expressing this allele. The purified protein exhibits a “hyper-helicase” unwinding activity in vitro. Using rapid quench, pre-steady state kinetic experiments we show the increased helicase activity of UvrD303 is due to an increase in the processivity of the unwinding reaction. We suggest that this mutation in the 2B subdomain results in a weakened interaction with the 1B subdomain, allowing the helicase to adopt a more open conformation. This is consistent with the idea that the 2B subdomain may have an autoregulatory role. The UvrD303 mutation may enable the helicase to unwind DNA via a “strand displacement” mechanism, which is similar to the mechanism used to processively translocate along single-stranded DNA, and the increased unwinding processivity may contribute directly to the antimutator phenotype.     

Identifying rare and common disease associated variants in genomic data using Parkinson’s disease as a model

Background

Genome-wide association studies have been successful in identifying common genetic variants for human diseases. However, much of the heritable variation associated with diseases such as Parkinson’s disease remains unknown suggesting that many more risk loci are yet to be identified. Rare variants have become important in disease association studies for explaining missing heritability. Methods for detecting this type of association require prior knowledge on candidate genes and combining variants within the region. These methods may suffer from power loss in situations with many neutral variants or causal variants with opposite effects.

Results

We propose a method capable of scanning genetic variants to identify the region most likely harbouring disease gene with rare and/or common causal variants. Our method assigns a score at each individual variant based on our scoring system. It uses aggregate scores to identify the region with disease association. We evaluate performance by simulation based on 1000 Genomes sequencing data and compare with three commonly used methods. We use a Parkinson’s disease case–control dataset as a model to demonstrate the application of our method.Our method has better power than CMC and WSS and similar power to SKAT-O with well-controlled type I error under simulation based on 1000 Genomes sequencing data. In real data analysis, we confirm the association of α-synuclein gene (SNCA) with Parkinson’s disease (p = 0.005). We further identify association with hyaluronan synthase 2 (HAS2, p = 0.028) and kringle containing transmembrane protein 1 (KREMEN1, p = 0.006). KREMEN1 is associated with Wnt signalling pathway which has been shown to play an important role for neurodegeneration in Parkinson’s disease.

Conclusions

Our method is time efficient and less sensitive to inclusion of neutral variants and direction effect of causal variants. It can narrow down a genomic region or a chromosome to a disease associated region. Using Parkinson’s disease as a model, our method not only confirms association for a known gene but also identifies two genes previously found by other studies. In spite of many existing methods, we conclude that our method serves as an efficient alternative for exploring genomic data containing both rare and common variants.

Electronic supplementary material

The online version of this article (doi:10.1186/s12929-014-0088-9) contains supplementary material, which is available to authorized users.     

Functional correlates of allelopathic potential in a successional plant community

Allelopathy, plant–plant interactions mediated through chemical production, is an active area of ecological research. Despite this widespread interest, we still lack community scale information on the prevalence of this interaction and the types of species that may be expected to be allelopathic. To address this research need, the allelopathic potential of 65 plant species from all stages of succession in the Piedmont region of New Jersey, USA, was determined with laboratory bioassays. The strength of each species’ allelopathic activity was then related to life form, origin, and fundamental plant traits. The vast majority of species tested exhibited significant allelopathic effects in the bioassays, with many of these having fairly strong effects. Overall, the allelopathic potential of species decreased with life span, roughly following the successional transitions from short-lived to long-lived herbs and to woody species. Herbaceous species on average were more allelopathic than woody species, but there was no difference between native and non-native species once life form was accounted for. In a principal components analysis, allelopathy was associated with other plant traits, but these relationships differed between woody and herbaceous species. Allelopathic potential was positively associated with plant height in herbaceous species, but negatively associated with height, leaf mass, and seed mass in woody species. These results indicate that allelopathy may be a quite common ecological strategy in plants and is equally common in both native and non-native species. The linkage of allelopathy with other plant functional traits suggests that allelopathy can and should be integrated into the broader suite of plant strategies that are studied.     

Impact of temperature on Na2Sr(PO4)F:Eu3+ phosphor

In this article, we report the synthesis of Na₂Sr_1‐x(PO₄)F:Eu_x phosphor via a combustion method. The influence of different annealing temperatures on the photoluminescence properties was investigated. The phosphor was excited at both 254 and 393 nm. Na₂Sr_1‐x(PO₄)F:Eu_x³⁺ phosphors emit strong orange and red color at 593 and 612 nm, respectively, under both excitation wavelengths. Na₂Sr_1‐x(PO₄)F:Eu_x³⁺ phosphors annealed at 1050°C showed stronger emission intensity compared with 600, 900 and 1200°C. Moreover, Na₂Sr_1‐x(PO₄)F:Eu_x³⁺ phosphor was found to be more intense when compared with commercial Y₂O₃:Eu³⁺ phosphor. Copyright © 2013 John Wiley & Sons, Ltd.     

Stretching Submicron Biomolecules with Constant-Force Axial Optical Tweezers

Optical tweezers have become powerful tools to manipulate biomolecular systems, but are increasingly difficult to use when the size of the molecules is <1 μm. Many important biological structures and processes, however, occur on the submicron length scale. Therefore, we developed and characterized an optical manipulation protocol that makes this length scale accessible by stretching the molecule in the axial direction of the laser beam, thus avoiding limiting artifacts from steric hindrances from the microscope coverslip and other surface effects. The molecule is held under constant mechanical tension by a combination of optical gradient forces and backscattering forces, eliminating the need for electronic feedback. We demonstrate the utility of this method through a measurement of the force-extension relationship of a 1298 bp ds-DNA molecule.     

Vegetation complexity—The influence of plant species diversity and plant structures on plant chemical complexity and arthropods

Vegetation complexity is characterized by two major traits, i.e., plant chemical and plant structural complexity. Plant species diversity strongly determines these traits. Furthermore, plant structures affect microclimatic conditions, which in turn influence the emission and dispersion of plant volatiles (e.g., chemical complexity). Plant volatile chemical complexity may significantly affect orientation of herbivorous and carnivorous arthropods. Therefore, the way in which plant chemical and plant structural complexity act “in concert” may influence foraging and mating success of arthropods, and thus, finally, community composition. This review emphasizes an integrative view on the relationship between plant species diversity, plant structural complexity, plant volatiles (chemical complexity) and their effects on arthropods. Three new hypotheses are raised, which predict possible relations between plant volatile complexity and plant species diversity: (1) saturation-, (2) step-by-step, (3) incoherence-hypothesis. We conclude that arthropod orientation in natural environments is strongly determined by the relationship between plant volatile diversity and plant species diversity. Furthermore, we emphasize that structural complexity of the vegetation affects plant volatile diversity and thus, arthropod orientation.We review available information on how insects actually respond to complexity during olfactory and visual search and ask for both laboratory and field studies to further unravel the mechanisms of interactions between vegetation traits and their impact on arthropod orientation.     

Erratum

Neurotransmitter receptor trafficking and the regulation of synaptic strength. Traffic 2001:2(7):437–448.     

Investigation of photosensitizing dyes for pathogen reduction in red cell suspensions

Despite recent advances in blood safety by careful donor selection and implementation of infectious disease testing, transmission of viruses, bacteria and parasites by transfusion can still rarely occur. One approach to reduce the residual risk from currently tested pathogens and to protect against the emergence of new ones is to investigate methods for pathogen inactivation. The use of photosensitizing dyes for pathogen inactivation has been studied in both red cell and platelet blood components. Optimal properties of sensitizing dyes for use in red cell suspensions include selection of dyes that traverse cell and viral membranes, bind to nucleic acids, absorb light in the red region of the spectrum, inactivate a wide range of pathogens, produce little red cell photodamage from dye not bound to nucleic acid and do not hemolyze red cells in the dark. Early research at the American Red Cross focused on the use of a class of dyes with rigid structures, such as the phenothiazine dyes, beginning with the prototypical sensitizer methylene blue. Results revealed that methylene blue phototreatment could inactivate extracellular virus, but resulted in undesirable defects in the red cell membrane that resulted in enhanced hemolysis that became evident during extended refrigerated blood storage. In addition, methylene blue phototreatment could neither inactivate intracellular viruses nor appreciably inactivate bacteria under conditions of extracellualar viral killing. Attempts to improve intracellular viral inactivation led to the investigations of more hydrophobic phenothiazines, such as methylene violet or dimethylmethylene blue. Although these dyes could inactivate intracellular virus, problems with increased red cell membrane damage and hemolysis persisted or increased. Further studies using red cell additive storage solutions containing high levels of the impermeable ion, citrate, to protect against colloidal osmotic hemolysis as well as competitive inhibitors to limit sensitizer binding to red cell membranes revealed that photoinduced hemolysis stemmed from dye bound to the red cell membrane as well as dye free in solution. Use of red cell additive solutions to prevent colloidal-osmotic hemolysis and use of novel flexible dyes that only act as sensitizers when bound to their targets are two techniques that currently are under investigation for reducing red cell damage. Ultimately, the decision to implement a photodynamic method for pathogen reduction will be determined by weighing the risks of unintended adverse consequences of the procedure itself, such as the potential for genotoxicity and allergic reactions, against the cost and benefits of its implementation.     

Stretching short sequences of DNA with constant force axial optical tweezers

Single-molecule techniques for stretching DNA of contour lengths less than a kilobase are fraught with experimental difficulties. However, many interesting biological events such as histone binding and protein-mediated looping of DNA, occur on this length scale. In recent years, the mechanical properties of DNA have been shown to play a significant role in fundamental cellular processes like the packaging of DNA into compact nucleosomes and chromatin fibers. Clearly, it is then important to understand the mechanical properties of short stretches of DNA. In this paper, we provide a practical guide to a single-molecule optical tweezing technique that we have developed to study the mechanical behavior of DNA with contour lengths as short as a few hundred basepairs. The major hurdle in stretching short segments of DNA is that conventional optical tweezers are generally designed to apply force in a direction lateral to the stage (see Fig. 1). In this geometry, the angle between the bead and the coverslip, to which the DNA is tethered, becomes very steep for submicron length DNA. The axial position must now be accounted for, which can be a challenge, and, since the extension drags the microsphere closer to the coverslip, steric effects are enhanced. Furthermore, as a result of the asymmetry of the microspheres, lateral extensions will generate varying levels of torque due to rotation of the microsphere within the optical trap since the direction of the reactive force changes during the extension. Alternate methods for stretching submicron DNA run up against their own unique hurdles. For instance, a dual-beam optical trap is limited to stretching DNA of around a wavelength, at which point interference effects between the two traps and from light scattering between the microspheres begin to pose a significant problem. Replacing one of the traps with a micropipette would most likely suffer from similar challenges. While one could directly use the axial potential to stretch the DNA, an active feedback scheme would be needed to apply a constant force and the bandwidth of this will be quite limited, especially at low forces. We circumvent these fundamental problems by directly pulling the DNA away from the coverslip by using a constant force axial optical tweezers. This is achieved by trapping the bead in a linear region of the optical potential, where the optical force is constant-the strength of which can be tuned by adjusting the laser power. Trapping within the linear region also serves as an all optical force-clamp on the DNA that extends for nearly 350 nm in the axial direction. We simultaneously compensate for thermal and mechanical drift by finely adjusting the position of the stage so that a reference microsphere stuck to the coverslip remains at the same position and focus, allowing for a virtually limitless observation period.