Food web structure changes with elevation but not rainforest stratum

Changes in species richness along elevational gradients are well documented. However, little is known about how trophic interactions between species and, in particular, the food webs that these interactions comprise, change with elevation. Here we present results for the first comparison of quantitative food webs in forest understorey and canopy along an elevational gradient. Replicate quantitative food webs were constructed for assemblages involving 23 species of cavity‐nesting Hymenoptera and 12 species of their parasitoids and kleptoparasites in subtropical rainforest in Australia. A total of 1589 insects were collected using trap nests across 20 plots distributed at sites ranging from 300 to 1100 m a.s.l. Insect abundance, insect diversity and parasitism rate generally decreased with increasing elevation. Food web structure significantly changed with elevation. In particular, weighted quantitative measures of linkage density, interaction evenness, nestedness (weighted NODF) and potential for enemy mediated interactions (PAC) decreased with increasing elevation, and network specialisation (H₂′) increased with increasing elevation, even after controlling for matrix size; but there was no change in weighted connectance. Changes in forest type and temperature along the elevational gradient are likely to be, at least partly, responsible for the patterns observed. We found no significant differences in insect abundance, insect diversity or parasitism rate between canopy and understorey. Furthermore, there were no differences in food web structure between strata. These results contribute further evidence to studies revealing changes in food web structure along natural environmental gradients and provide information that can potentially be used for predicting how communities may respond to climate change.     

Comparative shotgun proteomic analysis of Clostridium acetobutylicum from butanol fermentation using glucose and xylose

Background

Cytokinin is a plant hormone that plays a crucial role in several processes of plant growth and development. In recent years, major breakthroughs have been achieved in the elucidation of the metabolism, the signal perception and transduction, as well as the biological functions of cytokinin. An important activity of cytokinin is the involvement in chloroplast development and function. Although this biological function has already been known for 50 years, the exact mechanisms remain elusive.

Results

To elucidate the effects of altered endogenous cytokinin content on the structure and function of the chloroplasts, chloroplast subfractions (stroma and thylakoids) from transgenic Pssu-ipt and 35S:CKX1 tobacco (Nicotiana tabacum) plants with, respectively, elevated and reduced endogenous cytokinin content were analysed using two different 2-DE approaches. Firstly, thykaloids were analysed by blue-native polyacrylamide gel electrophoresis followed by SDS-PAGE (BN/SDS-PAGE). Image analysis of the gel spot pattern thus obtained from thylakoids showed no substantial differences between wild-type and transgenic tobacco plants. Secondly, a quantitative DIGE analysis of CHAPS soluble proteins derived from chloroplast subfractions indicated significant gel spot abundance differences in the stroma fraction. Upon identification by MALDI-TOF/TOF mass spectrometry, these proteins could be assigned to the Calvin-Benson cycle and photoprotective mechanisms.

Conclusion

Taken together, presented proteomic data reveal that the constitutively altered cytokinin status of transgenic plants does not result in any qualitative changes in either stroma proteins or protein complexes of thylakoid membranes of fully developed chloroplasts, while few but significant quantitative differences are observed in stroma proteins.     

High-resolution whole-genome association study of Parkinson disease

We performed a two-tiered, whole-genome association study of Parkinson disease (PD). For tier 1, we individually genotyped 198,345 uniformly spaced and informative single-nucleotide polymorphisms (SNPs) in 443 sibling pairs discordant for PD. For tier 2a, we individually genotyped 1,793 PD-associated SNPs (P<.01 in tier 1) and 300 genomic control SNPs in 332 matched case-unrelated control pairs. We identified 11 SNPs that were associated with PD (P<.01) in both tier 1 and tier 2 samples and had the same direction of effect. For these SNPs, we combined data from the case-unaffected sibling pair (tier 1) and case-unrelated control pair (tier 2) samples and employed a liberalization of the sibling transmission/disequilibrium test to calculate odds ratios, 95% confidence intervals, and P values. A SNP within the semaphorin 5A gene (SEMA5A) had the lowest combined P value (P=7.62 x 10(-6)). The protein encoded by this gene plays an important role in neurogenesis and in neuronal apoptosis, which is consistent with existing hypotheses regarding PD pathogenesis. A second SNP tagged the PARK11 late-onset PD susceptibility locus (P=1.70 x 10(-5)). In tier 2b, we also selected for genotyping additional SNPs that were borderline significant (P<.05) in tier 1 but that tested a priori biological and genetic hypotheses regarding susceptibility to PD (n=941 SNPs). In analysis of the combined tier 1 and tier 2b data, the two SNPs with the lowest P values (P=9.07 x 10(-6); P=2.96 x 10(-5)) tagged the PARK10 late-onset PD susceptibility locus. Independent replication across populations will clarify the role of the genomic loci tagged by these SNPs in conferring PD susceptibility.     

Vegetative characteristics of three low-lying Florida coastal rivers in relation to flow, light, salinity and nutrients

The Chassahowitzka, Homosassa and Crystal rivers along the central Gulf coast of Florida were studied from 1998 to 2000 to identify factors controlling the abundance and distribution of submersed aquatic vegetation (SAV). Each of these three low-lying coastal rivers are spring-fed and exhibit low to moderate absolute flow rates (flows in either direction because of tidal influences, 0.06–0.46ms^–1) with only 14 of the stations sampled for SAV having flow rates in excess of 0.25ms^–1. At those stations where flow rates exceeded 0.25ms–1, the substrate was generally comprised of exposed limestone outcroppings and did not provide a favorable habitat for either submersed macrophytes or macroalgae. The remaining sampling stations, where flow rates were less than 0.25ms–1, had suitable substrates (e.g. mud, mud/sand, and sand) for the colonization and subsequent growth of SAV. Light availability and salinity were determined to be major factors affecting the distribution and abundance of SAV. Sampling stations, where the percent of incident light at the surface reaching the substrate was less than 10, had little or no SAV biomass. Low SAV biomass was also linked to sites where annual average salinities exceeded 3.5. Nutrient loads and nutrient concentrations accounted for little variance in SAV biomass after accounting for flow and related substrate type, light and salinity. These latter factors control the distribution and abundance of SAV in these three Florida coastal rivers.     

Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density

Efforts in structural biology have targeted the systematic determination of all protein structures through experimental determination or modeling. In recent years, 3-D electron cryomicroscopy (cryoEM) has assumed an increasingly important role in determining the structures of these large macromolecular assemblies to intermediate resolutions (6–10 Å). While these structures provide a snapshot of the assembly and its components in well-defined functional states, the resolution limits the ability to build accurate structural models. In contrast, sequence-based modeling techniques are capable of producing relatively robust structural models for isolated proteins or domains. In this work, we developed and applied a hybrid modeling approach, utilizing cryoEM density and ab initio modeling to produce a structural model for the core domain of a herpesvirus structural protein, VP26. Specifically, this method, first tested on simulated data, utilizes the cryoEM density map as a geometrical constraint in identifying the most native-like models from a gallery of models generated by ab initio modeling. The resulting model for the core domain of VP26, based on the 8.5-Å resolution herpes simplex virus type 1 (HSV-1) capsid cryoEM structure and mutational data, exhibited a novel fold. Additionally, the core domain of VP26 appeared to have a complementary interface to the known upper-domain structure of VP5, its cognate binding partner. While this new model provides for a better understanding of the assembly and interactions of VP26 in HSV-1, the approach itself may have broader applications in modeling the components of large macromolecular assemblies.     

Overcoming original antigenic sin to generate new CD8 T cell IFN-gamma responses in an antigen-experienced host

The failure to mount effective immunity to virus variants in a previously virus-infected host is known as original antigenic sin. We have previously shown that prior immunity to a virus capsid protein inhibits induction by immunization of an IFN-gamma CD8+ T cell response to an epitope linked to the capsid protein. We now demonstrate that capsid protein-primed CD4+ T cells secrete IL-10 in response to capsid protein presented by dendritic cells, and deviate CD8+ T cells responding to a linked MHC class I-restricted epitope to reduce IFN-gamma production. Neutralizing IL-10 while delivering further linked epitope, either in vitro or in vivo, restores induction by immunization of an Ag-specific IFN-gamma response to the epitope. This finding demonstrates a strategy for overcoming inhibition of MHC class I epitopes upon immunization of a host already primed to Ag, which may facilitate immunotherapy for chronic viral infection or cancer.     

A comparison between aquatic birds of lakes and coastal rivers in Florida

Aquatic birds were counted on five Gulf coast Florida rivers to determine if these river systems supported densities, biomass and species richness similar to those found on Florida lakes. Forty-two species were identified and for the species that were found on both Florida streams and lakes similar densities and biomass were encountered. As with Florida lakes, stream bird abundance and species richness were higher in winter months than in summer months, a consequence of migratory bird populations. Total bird abundance, biomass per unit of phosphorus, and species richness per unit of area were similar to data collected on Florida lakes. Thus, Florida rivers are capable of supplying sufficient resources to maintain bird densities, biomass and species richness values similar to lakes of equal size and nutrient concentrations and are therefore important habitats for aquatic bird populations. An examination of individual habitat characteristics indicates that water depth was inversely correlated and submersed aquatic vegetation was positively correlated with bird density, biomass and species richness within the river systems. While both habitat characteristics are important they are also inversely related making it difficult to separate the individual significance of each characteristic.     

Postproduction Processing of Electrospun Fibres for Tissue Engineering

Electrospinning is a commonly used and versatile method to produce scaffolds (often biodegradable) for 3D tissue engineering.^{1, 2, 3} Many tissues in vivo undergo biaxial distension to varying extents such as skin, bladder, pelvic floor and even the hard palate as children grow. In producing scaffolds for these purposes there is a need to develop scaffolds of appropriate biomechanical properties (whether achieved without or with cells) and which are sterile for clinical use. The focus of this paper is not how to establish basic electrospinning parameters (as there is extensive literature on electrospinning) but on how to modify spun scaffolds post production to make them fit for tissue engineering purposes - here thickness, mechanical properties and sterilisation (required for clinical use) are considered and we also describe how cells can be cultured on scaffolds and subjected to biaxial strain to condition them for specific applications.Electrospinning tends to produce thin sheets; as the electrospinning collector becomes coated with insulating fibres it becomes a poor conductor such that fibres no longer deposit on it. Hence we describe approaches to produce thicker structures by heat or vapour annealing increasing the strength of scaffolds but not necessarily the elasticity. Sequential spinning of scaffolds of different polymers to achieve complex scaffolds is also described. Sterilisation methodologies can adversely affect strength and elasticity of scaffolds. We compare three methods for their effects on the biomechanical properties on electrospun scaffolds of poly lactic-co-glycolic acid (PLGA).Imaging of cells on scaffolds and assessment of production of extracellular matrix (ECM) proteins by cells on scaffolds is described. Culturing cells on scaffolds in vitro can improve scaffold strength and elasticity but the tissue engineering literature shows that cells often fail to produce appropriate ECM when cultured under static conditions. There are few commercial systems available that allow one to culture cells on scaffolds under dynamic conditioning regimes - one example is the Bose Electroforce 3100 which can be used to exert a conditioning programme on cells in scaffolds held using mechanical grips within a media filled chamber.⁴ An approach to a budget cell culture bioreactor for controlled distortion in 2 dimensions is described. We show that cells can be induced to produce elastin under these conditions. Finally assessment of the biomechanical properties of processed scaffolds cultured with or without cells is described.