Photodegradation influences litter decomposition rate in a humid tropical ecosystem, Brazil.

Solar radiation in general and UV radiation in particular have been recognized to stimulate plant litter decomposition through photochemical mineralization of organic molecules such as lignin and through facilitation of microbial decomposition in dryland ecosystems. However, little is known about how photodegradation may influence decomposition in other ecosystems not subject to moisture limitations and under what conditions photodegradation may be favored. Decomposition in humid tropical ecosystems is a complex process, and it can be influenced by a number of environmental factors that are distinct from arid and semi-arid ecosystems. To assess the mechanisms underlying photodegradation by ultraviolet B (UV-B) radiation in a humid tropical ecosystem, we designed a 300-day field experiment in a tropical site in Brazil with high levels of annual precipitation, compared to arid ecosystems, and exposed litter to three levels of radiation (full sun, UV-B removed, and shade) combined with a biocide treatment. Results show that after nearly one year of exposure, the microbial biomass was not affected by UV-B incidence, and this effect has not yet been fully understood for tropical ecosystems. Modeled using an exponential deceleration equation, the removal of UV-B radiation decelerated the plant litter decomposition rate for the control conditions by 21% compared to litter exposed to full sun. Interestingly, shaded litter exhibited similar mass loss compared to litter exposed to full sun. Furthermore, differences in the decay constant among radiation treatments due to the UV-B effect were independent of lignin loss. Overall, our study suggests that UV-B radiation contributed to plant litter decomposition through carbon losses but had no discernible effect on nitrogen, lignin, or cellulose loss specifically. Importantly, our results demonstrate that photodegradation occurs under humid tropical conditions, and further studies are necessary to examine the mechanisms of carbon loss.

Short-term facilitation of microbial litter decomposition by ultraviolet radiation.

Solar radiation plays an important role in carbon cycling by increasing the decomposition rates of plant litter and soil organic matter (i.e. photodegradation). Previous work suggests that exposure to radiation can facilitate microbial decomposition of litter by altering litter chemistry and consequently litter degradability (i.e. photopriming). However, it remains unclear to what extent photopriming contributes to litter decomposition processes and on what timescale photopriming operates. We conducted laboratory experiments to compare the effects of UV photopriming at two temporal scales (months versus days). In one experiment, we found that four months of UV exposure induced a significant but small (3-4%) mass loss in two of three litter species commonly found in California oak savanna; however, UV exposure did not alter litter degradability as measured by microbial respiration in an incubation experiment. We also found that UV exposure had limited effects on lignin and other cell wall structures, but one month of microbial decomposition (in absence of UV exposure) significantly reduced lignin ß-aryl ether inter-unit linkages and acetylated xylans. These results indicate that abiotic photodegradation alone was ineffective at breaking down lignin. In another experiment, litter of a common grass was exposed to either alternating UV radiation and dark conditions or constant darkness for 128days. We found that the alternating UV exposure increased litter CO2 production in both dark and UV phases over that observed in constant darkness. This led to a 35% greater release of CO2 from the alternating UV exposure treatment between days 65 and 128 of the experiment. These results demonstrate that alternating UV exposure with dark conditions is key to enabling photopriming on a timescale of days. Overall, we identify short-term photopriming as a novel mechanism behind photodegradation. Our results also challenge the conventional hypothesis that abiotic processes are primarily responsible for degrading lignin during photodegradation.

Impact of fog drip versus fog immersion on the physiology of Bishop pine saplings.

Fog-drip to the soil is the most obvious contribution of fog to the water budget of an ecosystem, but several studies provide convincing evidence that foliar absorption of fog water through leaf wetting events is also possible. The focus of our research was to assess the relative importance of fog drip and fog immersion (foliar wetting) on leaf gas-exchange rates and photosynthetic capacity of a coastal pine species, Bishop pine (Pinus muricata D.Don), a drought-sensitive species restricted to the fog belt of coastal California and offshore islands. In a controlled experiment, we manipulated fog water inputs to potted Bishop pine saplings during a 3 week dry-down period. Ten saplings were randomly assigned one of two fog treatments: (1) fog drip to the soil and canopy fog immersion, or (2) fog immersion alone. Five saplings were assigned the 'control' group and received no fog water inputs. We found that fog immersion alone significantly increased carbon assimilation rates and photosynthetic capacity of saplings as soil moisture declined compared with those that received no fog at all. The highest carbon assimilation rates were observed in saplings that also received fog drip. Soil moisture was 40% higher in the fog immersion compared with the control group during the dry-down, indicating a reduced demand for soil water in saplings that had only leaves wetted by canopy interception of fog. Leaf-level physiology is more strongly enhanced by fog drip compared with fog immersion, although the results of this study provide evidence that foliar absorption is a viable mechanism by which Bishop pines use fog water and that it can enhance instantaneous plant carbon gain and potentially whole plant productivity.

Coastal fog during summer drought improves the water status of sapling trees more than adult trees in a California pine forest.

Fog water inputs can offset seasonal drought in the Mediterranean climate of coastal California and may be critical to the persistence of many endemic plant species. The ability to predict plant species response to potential changes in the fog regime hinges on understanding the ways that fog can impact plant physiological function across life stages. Our study uses a direct metric of water status, namely plant water potential, to understand differential responses of adult versus sapling trees to seasonal drought and fog water inputs. We place these measurements within a water balance framework that incorporates the varying climatic and soil property impacts on water budgets and deficit. We conducted our study at a coastal and an inland site within the largest stand of the regionally endemic bishop pine (Pinus muricata D. Don) on Santa Cruz Island. Our results show conclusively that summer drought negatively affects the water status of sapling more than adult trees and that sapling trees are also more responsive to changes in shallow soil moisture inputs from fog water deposition. Moreover, between the beginning and end of a large, late-season fog drip event, water status increased more for saplings than for adults. Relative to non-foggy conditions, we found that fog water reduces modeled peak water deficit by 80 and 70 % at the inland and coastal sites, respectively. Results from our study inform mechanistically based predictions of how population dynamics of this and other coastal species may be affected by a warmer, drier, and potentially less foggy future.

Global-scale similarities in nitrogen release patterns during long-term decomposition.

Litter decomposition provides the primary source of mineral nitrogen (N) for biological activity in most terrestrial ecosystems. A 10-year decomposition experiment in 21 sites from seven biomes found that net N release from leaf litter is dominantly driven by the initial tissue N concentration and mass remaining regardless of climate, edaphic conditions, or biota. Arid grasslands exposed to high ultraviolet radiation were an exception, where net N release was insensitive to initial N. Roots released N linearly with decomposition and exhibited little net N immobilization. We suggest that fundamental constraints on decomposer physiologies lead to predictable global-scale patterns in net N release during decomposition.

Network analysis of human in-stent restenosis.

BACKGROUND: Recent successes in the treatment of in-stent restenosis (ISR) by drug-eluting stents belie the challenges still faced in certain lesions and patient groups. We analyzed human coronary atheroma in de novo and restenotic disease to identify targets of therapy that might avoid these limitations. METHODS AND RESULTS: We recruited 89 patients who underwent coronary atherectomy for de novo atherosclerosis (n=55) or in-stent restenosis (ISR) of a bare metal stent (n=34). Samples were fixed for histology, and gene expression was assessed with a dual-dye 22,000 oligonucleotide microarray. Histological analysis revealed significantly greater cellularity and significantly fewer inflammatory infiltrates and lipid pools in the ISR group. Gene ontology analysis demonstrated the prominence of cell proliferation programs in ISR and inflammation/immune programs in de novo restenosis. Network analysis, which combines semantic mining of the published literature with the expression signature of ISR, revealed gene expression modules suggested as candidates for selective inhibition of restenotic disease. Two modules are presented in more detail, the procollagen type 1 alpha2 gene and the ADAM17/tumor necrosis factor-alpha converting enzyme gene. We tested our contention that this method is capable of identifying successful targets of therapy by comparing mean significance scores for networks generated from subsets of the published literature containing the terms "sirolimus" or "paclitaxel." In addition, we generated 2 large networks with sirolimus and paclitaxel at their centers. Both analyses revealed higher mean values for sirolimus, suggesting that this agent has a broader suppressive action against ISR than paclitaxel. CONCLUSIONS: Comprehensive histological and gene network analysis of human ISR reveals potential targets for directed abrogation of restenotic disease and recapitulates the results of clinical trials of existing agents.

Pathway analysis of coronary atherosclerosis.

Large-scale gene expression studies provide significant insight into genes differentially regulated in disease processes such as cancer. However, these investigations offer limited understanding of multisystem, multicellular diseases such as atherosclerosis. A systems biology approach that accounts for gene interactions, incorporates nontranscriptionally regulated genes, and integrates prior knowledge offers many advantages. We performed a comprehensive gene level assessment of coronary atherosclerosis using 51 coronary artery segments isolated from the explanted hearts of 22 cardiac transplant patients. After histological grading of vascular segments according to American Heart Association guidelines, isolated RNA was hybridized onto a customized 22-K oligonucleotide microarray, and significance analysis of microarrays and gene ontology analyses were performed to identify significant gene expression profiles. Our studies revealed that loss of differentiated smooth muscle cell gene expression is the primary expression signature of disease progression in atherosclerosis. Furthermore, we provide insight into the severe form of coronary artery disease associated with diabetes, reporting an overabundance of immune and inflammatory signals in diabetics. We present a novel approach to pathway development based on connectivity, determined by language parsing of the published literature, and ranking, determined by the significance of differentially regulated genes in the network. In doing this, we identify highly connected "nexus" genes that are attractive candidates for therapeutic targeting and followup studies. Our use of pathway techniques to study atherosclerosis as an integrated network of gene interactions expands on traditional microarray analysis methods and emphasizes the significant advantages of a systems-based approach to analyzing complex disease.

Signature patterns of gene expression in mouse atherosclerosis and their correlation to human coronary disease.

The propensity for developing atherosclerosis is dependent on underlying genetic risk and varies as a function of age and exposure to environmental risk factors. Employing three mouse models with different disease susceptibility, two diets, and a longitudinal experimental design, it was possible to manipulate each of these factors to focus analysis on genes most likely to have a specific disease-related function. To identify differences in longitudinal gene expression patterns of atherosclerosis, we have developed and employed a statistical algorithm that relies on generalized regression and permutation analysis. Comprehensive annotation of the array with ontology and pathway terms has allowed rigorous identification of molecular and biological processes that underlie disease pathophysiology. The repertoire of atherosclerosis-related immunomodulatory genes has been extended, and additional fundamental pathways have been identified. This highly disease-specific group of mouse genes was combined with an extensive human coronary artery data set to identify a shared group of genes differentially regulated among atherosclerotic tissues from different species and different vascular beds. A small core subset of these differentially regulated genes was sufficient to accurately classify various stages of the disease in mouse. The same gene subset was also found to accurately classify human coronary lesion severity. In addition, this classifier gene set was able to distinguish with high accuracy atherectomy specimens from native coronary artery disease vs. those collected from in-stent restenosis lesions, thus identifying molecular differences between these two processes. These studies significantly focus efforts aimed at identifying central gene regulatory pathways that mediate atherosclerotic disease, and the identification of classification gene sets offers unique insights into potential diagnostic and therapeutic strategies in atherosclerotic disease.

Transcriptional profiling of in vitro smooth muscle cell differentiation identifies specific patterns of gene and pathway activation.

Mesodermal and epidermal precursor cells undergo phenotypic changes during differentiation to the smooth muscle cell (SMC) lineage that are relevant to pathophysiological processes in the adult. Molecular mechanisms that underlie lineage determination and terminal differentiation of this cell type have received much attention, but the genetic program that regulates these processes has not been fully defined. Study of SMC differentiation has been facilitated by development of the P19-derived A404 embryonal cell line, which differentiates toward this lineage in the presence of retinoic acid and allows selection for cells adopting a SMC fate through a differentiation-specific drug marker. We sought to define global alterations in gene expression by studying A404 cells during SMC differentiation with oligonucleotide microarray transcriptional profiling. Using an in situ 60-mer array platform with more than 20,000 mouse genes derived from the National Institute on Aging clone set, we identified 2,739 genes that were significantly upregulated after differentiation was completed (false-detection ratio <1). These genes encode numerous markers known to characterize differentiated SMC, as well as many unknown factors. We further characterized the sequential patterns of gene expression during the differentiation time course, particularly for known transcription factor families, providing new insights into the regulation of the differentiation process. Changes in genes associated with specific biological ontology-based pathways were evaluated, and temporal trends were identified for functional pathways. In addition to confirming the utility of the A404 model, our data provide a large-scale perspective of gene regulation during SMC differentiation.

UV radiation effects on plant growth and forage quality in a shortgrass steppe ecosystems.

Levels of UV were manipulated in a native shortgrass steppe using open-sided structures with tops that either passed or blocked wavelengths shorter than approximately 370 nm. Precipitation was controlled to create a drought or a very wet year. Subplots were either nondefoliated or defoliated to simulate grazing by livestock, which is the primary land use. Plant community productivity and forage quality were assessed in response to the two climate change variables (UV, precipitation) and grazing stress. Productivity and seasonal standing biomass of the dominant grass species were negatively affected by passing versus blocking UV, but only in the dry year. Another species was negatively affected by passing UV in the wet year, indicating the potential for future shifts in species composition. Forage quality for ruminants increased when UV was passed compared with blocked, as determined by in vitro digestible dry matter, depending on species and precipitation. Nitrogen concentrations and soluble and fiber components of vegetation also displayed some UV effects, but they were generally small and depended on species, season or amount of precipitation (or all). Grazing treatment had large positive effects on current-year productivity only in the wet year and some small positive effects on quality in both wet and dry years. Interactions between UV and grazing treatment were not observed.

Novel role for the potent endogenous inotrope apelin in human cardiac dysfunction.

BACKGROUND: Apelin is among the most potent stimulators of cardiac contractility known. However, no physiological or pathological role for apelin-angiotensin receptor-like 1 (APJ) signaling has ever been described. METHODS AND RESULTS: We performed transcriptional profiling using a spotted cDNA microarray with 12 814 unique clones on paired samples of left ventricle obtained before and after placement of a left ventricular assist device in 11 patients. The significance analysis of microarrays and a novel rank consistency score designed to exploit the paired structure of the data confirmed that natriuretic peptides were among the most significantly downregulated genes after offloading. The most significantly upregulated gene was the G-protein-coupled receptor APJ, the specific receptor for apelin. We demonstrate here using immunoassay and immunohistochemical techniques that apelin is localized primarily in the endothelium of the coronary arteries and is found at a higher concentration in cardiac tissue after mechanical offloading. These findings imply an important paracrine signaling pathway in the heart. We additionally extend the clinical significance of this work by reporting for the first time circulating human apelin levels and demonstrating increases in the plasma level of apelin in patients with left ventricular dysfunction. CONCLUSIONS: The apelin-APJ signaling pathway emerges as an important novel mediator of cardiovascular control.