Land-Use History and Contemporary Management Inform an Ecological Reference Model for Longleaf Pine Woodland Understory Plant Communities

Ecological restoration is frequently guided by reference conditions describing a successfully restored ecosystem; however, the causes and magnitude of ecosystem degradation vary, making simple knowledge of reference conditions insufficient for prioritizing and guiding restoration. Ecological reference models provide further guidance by quantifying reference conditions, as well as conditions at degraded states that deviate from reference conditions. Many reference models remain qualitative, however, limiting their utility. We quantified and evaluated a reference model for southeastern U.S. longleaf pine woodland understory plant communities. We used regression trees to classify 232 longleaf pine woodland sites at three locations along the Atlantic coastal plain based on relationships between understory plant community composition, soils (which broadly structure these communities), and factors associated with understory degradation, including fire frequency, agricultural history, and tree basal area. To understand the spatial generality of this model, we classified all sites together and for each of three study locations separately. Both the regional and location-specific models produced quantifiable degradation gradients–i.e., progressive deviation from conditions at 38 reference sites, based on understory species composition, diversity and total cover, litter depth, and other attributes. Regionally, fire suppression was the most important degrading factor, followed by agricultural history, but at individual locations, agricultural history or tree basal area was most important. At one location, the influence of a degrading factor depended on soil attributes. We suggest that our regional model can help prioritize longleaf pine woodland restoration across our study region; however, due to substantial landscape-to-landscape variation, local management decisions should take into account additional factors (e.g., soil attributes). Our study demonstrates the utility of quantifying degraded states and provides a series of hypotheses for future experimental restoration work. More broadly, our work provides a framework for developing and evaluating reference models that incorporate multiple, interactive anthropogenic drivers of ecosystem degradation.     

A Novel Method for Identification and Quantification of Consistently Differentially Methylated Regions

Advances in biotechnology have resulted in large-scale studies of DNA methylation. A differentially methylated region (DMR) is a genomic region with multiple adjacent CpG sites that exhibit different methylation statuses among multiple samples. Many so-called “supervised” methods have been established to identify DMRs between two or more comparison groups. Methods for the identification of DMRs without reference to phenotypic information are, however, less well studied. An alternative “unsupervised” approach was proposed, in which DMRs in studied samples were identified with consideration of nature dependence structure of methylation measurements between neighboring probes from tiling arrays. Through simulation study, we investigated effects of dependencies between neighboring probes on determining DMRs where a lot of spurious signals would be produced if the methylation data were analyzed independently of the probe. In contrast, our newly proposed method could successfully correct for this effect with a well-controlled false positive rate and a comparable sensitivity. By applying to two real datasets, we demonstrated that our method could provide a global picture of methylation variation in studied samples. R source codes to implement the proposed method were freely available at http://www.csjfann.ibms.sinica.edu.tw/eag/programlist/ICDMR/ICDMR.html.     

PCB-153 Shows Different Dynamics of Mobilisation from Differentiated Rat Adipocytes during Lipolysis in Comparison with PCB-28 and PCB-118

Background

Polychlorinated biphenyls (PCBs) are persistent organic pollutants. Due to their lipophilic character, they are preferentially stored within the adipose tissue. During the mobilisation of lipids, PCBs might be released from adipocytes into the bloodstream. However, the mechanisms associated with the release of PCBs have been poorly studied. Several in vivo studies followed their dynamics of release but the complexity of the in vivo situation, which is characterised by a large range of pollutants, does not allow understanding precisely the behaviour of individual congeners. The present in vitro experiment studied the impact of (i) the number and position of chlorine atoms of PCBs on their release from adipocytes and (ii) the presence of other PCB congeners on the mobilisation rate of such molecules.

Methodology/Principal Findings

Differentiated rat adipocytes were used to compare the behaviour of PCB-28, -118 and -153. Cells were contaminated with the three congeners, alone or in cocktail, and a lipolysis was then induced with isoproterenol during 12 hours. Our data indicate that the three congeners were efficiently released from adipocytes and accumulated in the medium during the lipolysis. Interestingly, for a same level of cell lipids, PCB-153, a hexa-CB with two chlorine atoms in ortho-position, was mobilised slower than PCB-28, a tri-CB, and PCB-118, a penta-CB, which are both characterised by one chlorine atom in ortho-position. It suggests an impact of the chemical properties of pollutants on their mobilisation during periods of negative energy balance. Moreover, the mobilisation of PCB congeners, taken individually, did not seem to be influenced by the presence of other congeners within adipocytes.

Conclusion/Significance

These results not only highlight the obvious mobilisation of PCBs from adipocytes during lipolysis, in parallel to lipids, but also demonstrate that the structure of congeners defines their rate of release from adipocytes.     

The eukaryotic protein kinase superfamily of the necrotrophic fungal plant pathogen,Sclerotinia sclerotiorum

Protein kinases have been implicated in the regulation of many processes that guide pathogen development throughout the course of infection. A survey of the Sclerotinia sclerotiorum genome for genes encoding proteins containing the highly conserved eukaryotic protein kinase (ePK) domain, the largest protein kinase superfamily, revealed 92 S. sclerotiorum ePKs. This review examines the composition of the S. sclerotiorum ePKs based on conserved motifs within the ePK domain family, and relates this to orthologues found in other filamentous fungi and yeasts. The ePKs are also discussed in terms of their proposed role(s) in aspects of host pathogenesis, including the coordination of mycelial growth/development and deployment of pathogenicity determinants in response to environmental stimuli, nutrients and stress.     

Digital image correlation and finite element modelling as a method to determine mechanical properties of human soft tissue in vivo

The mechanical properties of human soft tissue are crucial for impact biomechanics, rehabilitation engineering, and surgical simulation. Validation of these constitutive models using human data remains challenging and often requires the use of non-invasive imaging and inverse finite element (FE) analysis. Post-processing data from imaging methods such as tagged magnetic resonance imaging (MRI) can be challenging. Digital image correlation (DIC), however, is a relatively straightforward imaging method. DIC has been used in the past to study the planar and superficial properties of soft tissue and excised soft tissue layers. However, DIC has not been used to non-invasive study of the bulk properties of human soft tissue in vivo. Thus, the goal of this study was to assess the use of DIC in combination with FE modelling to determine the bulk material properties of human soft tissue. Indentation experiments were performed on a silicone gel soft tissue phantom. A two camera DIC setup was then used to record the 3D surface deformation. The experiment was then simulated using a FE model. The gel was modelled as Neo-Hookean hyperelastic, and the material parameters were determined by minimising the error between the experimental and FE data. The iterative FE analysis determined material parameters (μ=1.80 kPa, K=2999 kPa) that were in close agreement with parameters derived independently from regression to uniaxial compression tests (μ=1.71 kPa, K=2857 kPa). Furthermore the FE model was capable of reproducing the experimental indentor force as well as the surface deformation found (R²=0.81). It was therefore concluded that a two camera DIC configuration combined with FE modelling can be used to determine the bulk mechanical properties of materials that can be represented using hyperelastic Neo-Hookean constitutive laws.     

The importance of dispersal related and local factors in shaping the taxonomic structure of diatom metacommunities

To date, little is known about the relative importance of dispersal related versus local factors in shaping microbial metacommunities. A common criticism regarding existing datasets is that the level of taxonomic resolution might be too coarse to reliably assess microbial community structure and study biogeographical patterns. Moreover, few studies have assessed the importance of geographic distance between habitats, which may influence metacommunity dynamics through its effect on dispersal rates. We applied variation partitioning analyses to 15 separate regional datasets on diatoms found in lakes in Eurasia, Africa and Antarctica. These analyses quantified the relative contributions of dispersal related and local factors in determining patterns of taxonomic turnover at the species and at the genus level. In general, results were similar at both taxonomic levels. Local environmental factors accounted for most of the explained variation (median=21%), whereas dispersal related factors were much less important (median of significant fractions=5.5% variation explained) and failed to significantly explain any variation, independent of the environmental variables, in the majority of the datasets. However, the amount of variation explained by dispersal related factors increased with increasing geographic distance and increasing taxonomic resolution. We extrapolated our regional scale observations to the global scale by combining the regional datasets into a global dataset comprising 1039 freshwater lakes from both hemispheres and spanning a geographic distance of over 19 000  km. At this global scale, taxonomic turnover was lowest in highly connected habitats, once environmental factors were partialled out. In common with many other studies of macro-organisms, these analyses showed that both dispersal related and local variables significantly contribute to the structure of global lacustrine diatom communities.     

Synthesis of functionalized 1,8-naphthyridinones and their evaluation as novel, orally active CB1 receptor inverse agonists

Synthesis, SAR, and binding affinities are described for a new class of 1,8-naphthyridinone CB1 receptor specific inverse agonists. Food intake, knockout mouse, and pharmacokinetic evaluation of 14 indicate that this compound is an effective orally active modulator of CB1.     

Synthesis and structure-activity relationship of a novel, achiral series of TNF-alpha converting enzyme inhibitors

A novel series of achiral TNF-alpha converting enzyme (TACE) inhibitors has been discovered. These compounds exhibited activities from 0.35 to 11nM in a porcine TACE assay and inhibited TNF-alpha production in an LPS-stimulated whole blood assay with an IC(50) value of 23nM for the most potent one. They also have excellent selectivities over related metalloproteases including aggrecanases.     

Nitric oxide production by nurse shark (Ginglymostoma cirratum) and clearnose skate (Raja eglanteria) peripheral blood leucocytes

Reactive nitrogen intermediates, such as nitric oxide (NO), are important immunomodulators in vertebrate immune systems, but have yet to be identified as mediators of host defence in any member of class Chondrichthyes, the cartilaginous fishes. In the present study, production of NO by nurse shark (Ginglymostoma cirratum) peripheral blood leucocytes (PBL) stimulated with bacterial cell wall lipopolysaccharide (LPS) was investigated. PBL were cultured for 24 to 96 h following stimulation with LPS at concentrations ranging from 0 to 25 microg ml(-1), in both serum-supplemented and serum-free culture conditions. Production of NO was measured indirectly using the Griess reaction, with maximal NO production occurring after 72 h using 10% FBS and 10 microg LPS ml(-1). Application of these culture conditions to PBL from another cartilaginous fish (clearnose skate, Raja eglanteria) resulted in a similar NO response. Addition of a specific inhibitor of inducible nitric oxide synthase (iNOS), L-N(6)-(1-iminoethyl)lysine (L-NIL), resulted in a significant decrease in the production of NO by PBL from both species.