Correlation of Aging and Segmental Choroidal Thickness Measurement using Swept Source Optical Coherence Tomography in Healthy Eyes

Purpose

To assess and compare choroidal thickness changes related to aging, we determined whether changes are due to thinning of the choriocapillaris plus Sattler''s (CS) layer and/or the large vessel layer in healthy eyes using swept-source optical coherence tomography (SS-OCT) at a wavelength of 1,050-nm.

Methods

We studied 115 normal eyes of 115 healthy volunteers, all with refractive errors of less than -6 diopters. All 115 eyes underwent analysis of choroidal thickness at the fovea, the CS layer and the large choroidal vessel layer. In 68 of the 115 eyes, choroidal thickness was determined at five sites (the fovea, and superior, inferior, nasal, and temporal sites) using SS-OCT with an Early Treatment of Diabetic Retinopathy grid scan.

Results

Total choroidal thicknesses at each of the five sites were related to subject age (P<0.0001). The choroid was thinnest at the nasal site, followed by the temporal, inferior, superior and finally the subfoveal site itself. The total choroidal thickness at the nasal site was significantly less than those at the other four sites (p<0.05). The CS layer showed thinning which correlated with age (P<0.0001). The thickness of the choroidal large vessel layer also decreased with age (p = 0.02). Subfoveal choroidal thickness was calculated as follows: 443.89–2.98×age (μm) (P<0.0001).

Conclusion

Subfoveal choroidal thickness decreases by 2.98 μm each year. Total choroidal thickness diminishes with age. The CS and large vessel layers of the choroid at the subfovea showed significant decreases, though only the former correlated strongly with age.     

The Arabidopsis thaliana cysteine-rich receptor-like kinases CRK6 and CRK7 protect against apoplastic oxidative stress

Receptor-like kinases are important regulators of many different processes in plants. Despite their large number only a few have been functionally characterized. One of the largest subgroups of receptor-like kinases in Arabidopsis is the cysteine-rich receptor like kinases (CRKs). High sequence similarity among the CRKs has been suggested as major cause for functional redundancy. The genomic localization of CRK genes in back-to-back repeats has made their characterization through mutant analysis unpractical. Expression profiling has linked the CRKs with reactive oxygen species, important signaling molecules in plants. Here we have investigated the role of two CRKs, CRK6 and CRK7, and analyzed their role in extracellular ROS signaling. CRK6 and CRK7 are active protein kinases with differential preference for divalent cations. Our results suggest that CRK7 is involved in mediating the responses to extracellular but not chloroplastic ROS production.     

sFas levels increase in response to cisplatin-based chemotherapy in lung cancer patients

The Fas/Fas Ligand (FasL) system and survivin have counteracting roles in cell survival. Therefore, we explored the role of circulating soluble Fas (sFas) and the tissue levels of Fas and survivin with regard to response to chemotherapy in lung cancer patients. Serum samples from 52 lung cancer patients and 54 control subjects (19 benign lung disease and 35 healthy control subjects) were collected prior to and 24 and 48 h after chemotherapy. sFas was statistically significantly higher in the cancer group than that in the control groups (p < 0.001). Baseline (before chemotherapy) sFas values showed a statistically significant inverse correlation with overall survival (r = ?0.599, p < 0.001). There was a significant increase in serum sFas levels 24 h after treatment (p < 0.05). Contrarily, tissue levels of Fas and survivin were not changed following the chemotherapy (p > 0,05). In conclusion, increased sFas may be an indicator of poor outcome in lung cancer patients. However, cisplatin‐based chemotherapy may not be effective via neither the Fas/FasL system nor survivin pathway. Indeed, larger sample size is required for further evaluation. Copyright © 2010 John Wiley & Sons, Ltd.     

Multi-element fingerprinting and high throughput sequencing identify multiple elements that affect fungal communities in Quercus macrocarpa foliage

Diverse fungal mutualists, pathogens and saprobes colonize plant leaves. These fungi face a complex environment, in which stochastic dispersal interplays with abiotic and biotic filters. However, identification of the specific factors that drive the community assembly seems unattainable. We mined two broad data sets and identified chemical elements, to which dominant molecular operational taxonomic units (OTUs) in the foliage of a native tree respond most extremely. While many associations could be identified, potential complicating issues emerged. Those were related to unevenly distributed OTU frequency data, a large number of potentially explanatory variables and the disproportionate effects of outlier observations.Key words: community assembly, environmental filter, fungi, heavy metal enrichment, nutrient enrichment, oak, Quercus macrocarpaHyperdiverse fungal communities inhabit the foliage of most plants^1,2 and these fungal communities have been reported for virtually every plant that has been examined.³ Baas-Becking hypothesis states that environment selects microbial communities from the abundant and possibly globally distributed propagule pools.⁴ Although the foliage-associated communities—like other microbial communities—are suspected to be sensitive to environmental drivers, determination of the mechanisms that control the assembly of these foliar communities has remained difficult and elusive. Some of the proposed mechanisms include distance limitations to propagule dispersal,^5–7 volume limitations to propagule loads,⁷ or limitations set by the environmental conditions either on the scale of the site of fungal colonization⁸ or more broadly on a landscape level.^6,9 The forces that may control the fungal community assembly are overlaid by additional biotic controls that include compatibilities between the fungi and host species^10,11 or genotypes^6,12 and the competitive or facilitative interactions among the component fungal genotypes.^6,10–13 Although a variety of potential controls for the foliage-associated fungal communities have been speculated, very little consensus exists on the relative importance of the different drivers. For example, while macronutrient and heavy metal enrichment may have an influence on the composition fungal communities¹⁴ and populations,¹⁵ relative importance of various chemical elements in the foliage remains yet to be investigated.To evaluate the use of multi-element fingerprinting data produced by Inductively Coupled Plasma Mass Spectrometry (ICP-MS) in combination with high throughput 454-pyrosequencing for determining influential chemical elements in structuring of the leaf-associated fungal communities, we mined a recent dataset¹⁶ that explored the effects of urbanization on the diversity and composition of the fungal communities associated with a native tree Quercus macrocarpa. From a total list of more than 700 non-singleton fungal OTUs, we selected fifty with highest overall frequency to provide an observationrich dataset for elemental effect assessment; these OTUs accounted for 84.5% of all sequences. Even so, many of these OTUs had a number of zero frequencies (Fig. 1), highlighting one of the difficulties in the use of environmental sequencing data. We omitted one OTU (OTU630 with a likely affinity to Trimmatostroma cordae [Mycosphaerellaceae]) that was strongly affected by the original land use design (urbanization; Wilcoxon rank sum test with a Bonferroni adjustment) and therefore unlikely to be representative for the present analyses of elemental drivers. This OTU was replaced with one with the next highest frequency. The frequencies of these 50 OTUs were investigated in the context of concentrations for 29 elements after the omission of five (Ag, Au, C, δ¹³C, δ¹⁵N) in the final analyses because of their strong association with the land use or the difficulty of finding a biological relevance. Of the remaining elements three (Fe, Cr and Ni) had pairwise correlations exceeding 0.98 between the three pairings; others showed no similar high correlations. To allow comparable evaluation across the broad array of elements, all concentrations were standardized to have a mean equal to zero and a standard deviation equal to one.Open in a separate windowFigure 1Rank-ordered distribution of observed frequencies for those OTU s whose frequency had an extreme slope when associated with the concentrations of one or more chemical elements in the mixed effects model. The asterisk denotes one extreme frequency for OTU 313 with a value 0.8636. Numbers in parentheses indicate the number of observations with a frequency equal to zero. The OTU s were assigned to approximate taxa using BLAST:²⁰ 425: Alternaria alternata (Pleosporaceae); 46: Phoma glomerata (Pleosporaceae); 686: Aureobasidium pullulans (Dothioraceae); 520: Davidiella tassiana (Davidiellaceae); 567: Cladosporioum tenuissimum (Davidiellaceae); 313 Oidium heveae (mitosporic Erysiphaceae); 586: Erysiphe hypogena (Erysiphaceae); 671: Mycosphaerella microsora (Mycosphaerellaceae); 555: Pestalotiopsis sp. (Amphisphaeriaceae); 607: Pleiochaeta setosa (incertae sedis).To rank elements according to their magnitude of association with the abundance of each OTU, a total of 1,450 models (50 OTUs times 29 elements) relating element concentration to OTU abundance were fit to the data. For each model, OTU frequency was the dependent variable, element concentration and time (a factor with three levels) were fixed effects, and—to account for the spatial arrangement of the experimental units—random effects associated with tree nested within site were included in the error structure. Time by element interactions were also investigated and tested using a likelihood ratio test. These mixed effect models were fit using R and the package lme4 (www.rproject.org).Statistical “tests of significance” that produce p-values can be sensitive to assumptions or outliers. Because of this and the fact that our analyses evaluated a total of 1,450 models, p-values themselves were not considered a reliable measure of importance when associating elements with OTU frequency. Instead, we emphasized metrics that highlight extraordinary findings rather than rely on tests of statistical significance. This approach facilitates finding few elements that have the strongest effect on OTU frequency. Note that the use of standardized element concentrations (above) provided slope coefficients that are comparable across all models. “Extreme slopes”, i.e., models where the OTU response to element concentration was strongest, were identified as those with estimated slope coefficients in the lower or upper 2.5 percentile, i.e., those farther than 1.8 standard deviations from the mean across all estimated slopes (Fig. 2). Using this approach, we identified a total of 69 models with extreme slopes (Open in a separate windowFigure 2Distribution of estimated slopes (i.e., the slope for element concentration) for a model relating OTU frequency to element concentration, time and a concentration by time interaction, including a tree-nested-within-site random effect. The mean across all 1,450 OTU s is approximately zero; the two vertical lines identify upper and lower 2.5 percentiles, beyond which the slopes were considered extreme (large black symbols). The horizontal line identifies the cut off maximum leverage (0.24), above which the slopes were considered to have observations with high leverage. Models with observations with a high leverage were tested for extreme slopes by refitting without those observations. Models are ranked from bottom to top in order of increasing leverage and the element for which the high-leverage observations and extreme slopes were recorded are identified on the right y-axis.

Table 1

Slopes identified as extreme in our analyses

Ecosystem services–A tool for sustainable management of human–environment systems. Case study Finnish Forest Lapland

The concept of ecosystem services (ESs) is a relatively new scientific methodology, offering a possible approach to the prevention of ecological problems caused by human action and to the resolution of conflicts arising from land-use questions. Since ESs were launched as a major conceptual tool in the Millennium Ecosystem Assessment (MA, 2005), interest in them has been increasing. Despite the scientific as well as economic and political enthusiasm for the ES approach, only few case studies have as yet been published. We studied the interface between ESs and landscape planning in Forest Lapland, in northern Finland. In the article, we present a methodology and various databases which can be used in applied research on ESs. We classify the ESs offered by various biotopes of the study area, and examine the effects of different land-use forms on the provision of ESs. On the basis of our results, we suggest possible uses of the European CORINE land cover database in case studies.     

The Potential Role of Stream Habitat Restoration in Facilitating Salmonid Invasions: A Habitat‐Hydraulic Modeling Approach

Many successful invasions have taken place in systems where harmful disturbance has changed habitat conditions. However, less attention has been paid to the role of habitat restoration, which modifies habitats and thus also has the potential to facilitate invasions. We examined whether in‐stream habitat restorations have the potential to either facilitate or resist invasion by two widely introduced non‐native stream salmonids, Salvelinus fontinalis Mitchill and Oncorhynchus mykiss Walbaum, in Finland. A physical habitat simulation system was used to calculate whether the habitat area for the target species increased or decreased following the restorations. For comparison, we also reported results for four native stream fish species. The simulations showed that the restored streams provided the highest amount of usable habitat area for the native species, particularly for Salmo salar L. and Gottus gobio L. However, it was interesting to note that the restorations significantly increased habitat quality for the two non‐native species, especially at low flows. Nevertheless, the non‐native species had the lowest amount of usable habitat area overall. The modeling results indicated that not only habitat destruction but also habitat restoration could contribute to the spread of non‐native species. Fisheries and wildlife managers should be aware of the possibility, when restoring habitats in order to preserve native ecosystems, that non‐native species could manage to gain a foothold in restored habitats and use them as population sources for further spread. Knowing the widespread negative effect of non‐native species, this risk should not be underestimated.     

Soil Fungal Communities Underneath Willow Canopies on a Primary Successional Glacier Forefront: rDNA Sequence Results Can Be Affected by Primer Selection and Chimeric Data

Soil fungal communities underneath willow canopies that had established on the forefront of a receding glacier were analyzed by cloning the polymerase chain reaction (PCR)-amplified partial small subunit (18S) of the ribosomal (rRNA) genes. Congruence between two sets of fungus-specific primers targeting the same gene region was analyzed by comparisons of inferred neighbor-joining topologies. The importance of chimeric sequences was evaluated by Chimera Check (Ribosomal Database Project) and by data reanalyses after omission of potentially chimeric regions at the 5'- and 3'-ends of the cloned amplicons. Diverse communities of fungi representing Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota were detected. Ectomycorrhizal fungi comprised a major component in the early plant communities in primary successional ecosystems, as both primer sets frequently detected basidiomycetes (Russulaceae and Thelephoraceae) forming mycorrhizal symbioses. Various ascomycetes (Ophiostomatales, Pezizales, and Sordariales) of uncertain function dominated the clone libraries amplified from the willow canopy soil with one set of primers, whereas the clone libraries of the amplicons generated with the second primer set were dominated by basidiomycetes. Accordingly, primer bias is an important factor in fungal community analyses using DNA extracted from environmental samples. A large proportion (>30%) of the cloned sequences were concluded to be chimeric based on their changing positions in inferred phylogenies after omission of possibly chimeric data. Many chimeric sequences were positioned basal to existing classes of fungi, suggesting that PCR artifacts may cause frequent discovery of new, higher level taxa (order, class) in direct PCR analyses. Longer extension times during the PCR amplification and a smaller number of PCR cycles are necessary precautions to allow collection of reliable environmental sequence data.     

Biosynthesis of hyperforin and adhyperforin from amino acid precursors in shoot cultures of Hypericum perforatum

Hyperforin and adhyperforin contribute to the antidepressant effects of Hypericum perforatum. The involvement of branched-chain amino acids in the biosynthesis of hyperforin and adhyperforin was demonstrated in H. perforatum shoot cultures. L-[U-(13)C(5)]Valine and L-[U-(13)C(6)]isoleucine, upon administration to the shoot cultures, were incorporated into acyl side chain of hyperforin and adhyperforin, respectively. Feeding the shoot cultures with unlabelled L-isoleucine at a concentration of 2mM induced a 3.7-fold increase in the production of adhyperforin. The addition of 3mM L-threonine, a precursor of isoleucine, stimulated a 2.0-fold increase in the accumulation of adhyperforin. The administration of L-valine at concentrations of 0-5mM had no stimulating effect on the hyperforin production in H. perforatum shoot cultures.     

Gamma interferon blocks gammaherpesvirus reactivation from latency in a cell type-specific manner

Gammaherpesviruses are important pathogens whose lifelong survival in the host depends critically on their capacity to establish and reactivate from latency, processes regulated by both viral genes and the host immune response. Previous work has demonstrated that gamma interferon (IFN-gamma) is a key regulator of chronic infection with murine gammaherpesvirus 68 (gammaHV68), a virus that establishes latent infection in B lymphocytes, macrophages, and dendritic cells. In mice deficient in IFN-gamma or the IFN-gamma receptor, gammaHV68 gene expression is altered during chronic infection, and peritoneal cells explanted from these mice reactivate more efficiently ex vivo than cells derived from wild-type mice. Furthermore, treatment with IFN-gamma inhibits reactivation of gammaHV68 from latently infected wild-type peritoneal cells, and depletion of IFN-gamma from wild-type mice increases the efficiency of reactivation of explanted peritoneal cells. These profound effects of IFN-gamma on chronic gammaHV68 latency and reactivation raise the question of which cells respond to IFN-gamma to control chronic gammaHV68 infection. Here, we show that IFN-gamma inhibited reactivation of peritoneal cells and spleen cells harvested from mice lacking B lymphocytes, but not wild-type spleen cells, suggesting that IFN-gamma may inhibit reactivation in a cell type-specific manner. To directly test this hypothesis, we expressed the diphtheria toxin receptor specifically on either B lymphocytes or macrophages and used diphtheria toxin treatment to deplete these specific cells in vivo and in vitro after establishing latency. We demonstrate that macrophages, but not B cells, are responsive to IFN-gamma-mediated suppression of gammaHV68 reactivation. These data indicate that the regulation of gammaherpesvirus latency by IFN-gamma is cell type specific and raise the possibility that cell type-specific immune deficiency may alter latency in distinct and important ways.