Relationship between foliar composition of red-pine and jack-pine seedlings and vulnerability to Lophodermium needle-cast disease

Summary The Mn and Al content of needles from two-year-old jack pine (Pinus banksiana) seedlings was found to be more than twice that of red pine (Pinus resinosa). It is speculated that the high Mn and Al content of jack pine seedlings may impart some degree of resistance to needle cast disease caused byLophodermium pinastri. Contribution from the Soils Dept., Univ. of Wis., Madison, in cooperation with and supported in part by the Wisconsin Dept. of Natural Resources. Publication approved by the Director of the Wisconsin Agricultural Experiment Station.     

Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers

Background

Accurate outcome prediction in neuroblastoma, which is necessary to enable the optimal choice of risk-related therapy, remains a challenge. To improve neuroblastoma patient stratification, this study aimed to identify prognostic tumor DNA methylation biomarkers.

Results

To identify genes silenced by promoter methylation, we first applied two independent genome-wide methylation screening methodologies to eight neuroblastoma cell lines. Specifically, we used re-expression profiling upon 5-aza-2''-deoxycytidine (DAC) treatment and massively parallel sequencing after capturing with a methyl-CpG-binding domain (MBD-seq). Putative methylation markers were selected from DAC-upregulated genes through a literature search and an upfront methylation-specific PCR on 20 primary neuroblastoma tumors, as well as through MBD- seq in combination with publicly available neuroblastoma tumor gene expression data. This yielded 43 candidate biomarkers that were subsequently tested by high-throughput methylation-specific PCR on an independent cohort of 89 primary neuroblastoma tumors that had been selected for risk classification and survival. Based on this analysis, methylation of KRT19, FAS, PRPH, CNR1, QPCT, HIST1H3C, ACSS3 and GRB10 was found to be associated with at least one of the classical risk factors, namely age, stage or MYCN status. Importantly, HIST1H3C and GNAS methylation was associated with overall and/or event-free survival.

Conclusions

This study combines two genome-wide methylation discovery methodologies and is the most extensive validation study in neuroblastoma performed thus far. We identified several novel prognostic DNA methylation markers and provide a basis for the development of a DNA methylation-based prognostic classifier in neuroblastoma.     

Targeted subfield switchgrass integration could improve the farm economy,water quality,and bioenergy feedstock production

Progress on reducing nutrient loss from annual croplands has been hampered by perceived conflicts between short‐term profitability and long‐term stewardship, but these may be overcome through strategic integration of perennial crops. Perennial biomass crops like switchgrass can mitigate nitrate‐nitrogen (NO₃‐N) leaching, address bioenergy feedstock targets, and – as a lower‐cost management alternative to annual crops (i.e., corn, soybeans) – may also improve farm profitability. We analyzed publicly available environmental, agronomic, and economic data with two integrated models: a subfield agroecosystem management model, Landscape Environmental Assessment Framework (LEAF), and a process‐based biogeochemical model, DeNitrification‐DeComposition (DNDC). We constructed a factorial combination of profitability and NO₃‐N leaching thresholds and simulated targeted switchgrass integration into corn/soybean cropland in the agricultural state of Iowa, USA. For each combination, we modeled (i) area converted to switchgrass, (ii) switchgrass biomass production, and (iii) NO₃‐N leaching reduction. We spatially analyzed two scenarios: converting to switchgrass corn/soybean cropland losing >US$ 100 ha^?1 and leaching >50 kg ha^?1 (‘conservative’ scenario) or losing >US$ 0 ha^?1 and leaching >20 kg ha^?1 (‘nutrient reduction’ scenario). Compared to baseline, the ‘conservative’ scenario resulted in 12% of cropland converted to switchgrass, which produced 11 million Mg of biomass and reduced leached NO₃‐N 18% statewide. The ‘nutrient reduction’ scenario converted 37% of cropland to switchgrass, producing 34 million Mg biomass and reducing leached NO₃‐N 38% statewide. The opportunity to meet joint goals was greatest within watersheds with undulating topography and lower corn/soybean productivity. Our approach bridges the scales at which NO₃‐N loss and profitability are usually considered, and is informed by both mechanistic and empirical understanding. Though approximated, our analysis supports development of farm‐level tools that can identify locations where both farm profitability and water quality improvement can be achieved through the strategic integration of perennial vegetation.     

Evidence for two distinct epitopes within collagen for activation of murine platelets

It has recently been shown that the monoclonal antibody JAQ1 to murine glycoprotein VI (GPVI) can cause aggregation of mouse platelets upon antibody cross-linking and that collagen-induced platelet aggregation can be inhibited by preincubation of platelets with JAQ1 in the absence of cross-linking (Nieswandt, B., Bergmeier, W., Schulte, V., Rackebrandt, K., Gessner, J. E., and Zirngibl, H. (2000) J. Biol. Chem. 275, 23998-24002). In the present study, we have shown that cross-linking of GPVI by JAQ1 results in tyrosine phosphorylation of the same profile of proteins as that induced by collagen, including the Fc receptor (FcR) gamma-chain, Syk, LAT, SLP-76, and phospholipase C gamma 2. In contrast, platelet aggregation and tyrosine phosphorylation of these proteins were inhibited when mouse platelets were preincubated with JAQ1 in the absence of cross-linking and were subsequently stimulated with a collagen-related peptide (CRP) that is specific for GPVI and low concentrations of collagen. However, at higher concentrations of collagen, but not CRP, aggregation of platelets and tyrosine phosphorylation of the above proteins (except for the adapter LAT) is re-established despite the presence of JAQ1. These observations suggest that a second activatory binding site, which is distinct from the CRP binding site on GPVI on mouse platelets, is occupied in the presence of high concentrations of collagen. Although this could be a second site on GPVI that is activated by a novel motif within the collagen molecule, the absence of LAT phosphorylation in response to collagen in the presence of JAQ1 suggests that this is more likely to be caused by activation of a second receptor that is also coupled to the FcR gamma-chain. The possibility that this response is mediated by a receptor that is not coupled to FcR gamma-chain is excluded on the grounds that aggregation is absent in platelets from FcR gamma-chain-deficient mice.     

Rhodocytin (aggretin) activates platelets lacking alpha(2)beta(1) integrin, glycoprotein VI, and the ligand-binding domain of glycoprotein Ibalpha

Although alpha(2)beta(1) integrin (glycoprotein Ia/IIa) has been established as a platelet collagen receptor, its role in collagen-induced platelet activation has been controversial. Recently, it has been demonstrated that rhodocytin (also termed aggretin), a snake venom toxin purified from the venom of Calloselasma rhodostoma, induces platelet activation that can be blocked by monoclonal antibodies against alpha(2)beta(1) integrin. This finding suggested that clustering of alpha(2)beta(1) integrin by rhodocytin is sufficient to induce platelet activation and led to the hypothesis that collagen may activate platelets by a similar mechanism. In contrast to these findings, we provided evidence that rhodocytin does not bind to alpha(2)beta(1) integrin. Here we show that the Cre/loxP-mediated loss of beta(1) integrin on mouse platelets has no effect on rhodocytin-induced platelet activation, excluding an essential role of alpha(2)beta(1) integrin in this process. Furthermore, proteolytic cleavage of the 45-kDa N-terminal domain of glycoprotein (GP) Ibalpha either on normal or on beta(1)-null platelets had no significant effect on rhodocytin-induced platelet activation. Moreover, mouse platelets lacking both alpha(2)beta(1) integrin and the activating collagen receptor GPVI responded normally to rhodocytin. Finally, even after additional proteolytic removal of the 45-kDa N-terminal domain of GPIbalpha rhodocytin induced aggregation of these platelets. These results demonstrate that rhodocytin induces platelet activation by mechanisms that are fundamentally different from those induced by collagen.     

Molecular systematics and phylogeography of Amazonian poison frogs of the genus Dendrobates

The study of Amazonian biodiversity requires detailed knowledge of the phylogenetic relationships of closely related taxa distributed across Amazonia. The Amazonian poison frogs of the genus Dendrobates have undergone many taxonomic revisions, but the phylogenetic relationships within this group remain poorly understood. Most previous classifications were based on morphology and skin toxin analyses, with limited use of DNA sequence data. Using mtDNA sequence data from four gene regions (cytochrome b, cytochrome oxidase I, 16S rRNA, and 12S rRNA), we present a molecular phylogenetic analysis of the evolutionary relationships within a representative group of Amazonian Dendrobates. We use the resulting phylogenetic hypothesis to investigate different biogeographic hypotheses concerning genetic divergence and species diversity in Amazonia. The results of the analysis support the presence of ancient paleogeographic barriers to gene flow between eastern and western Amazonia, and indicate substantial genetic divergence between species found in the northern and southern regions of western Amazonia.     

DISENTANGLING THE EFFECTS OF KEY INNOVATIONS ON THE DIVERSIFICATION OF BROMELIOIDEAE (BROMELIACEAE)

The evolution of key innovations, novel traits that promote diversification, is often seen as major driver for the unequal distribution of species richness within the tree of life. In this study, we aim to determine the factors underlying the extraordinary radiation of the subfamily Bromelioideae, one of the most diverse clades among the neotropical plant family Bromeliaceae. Based on an extended molecular phylogenetic data set, we examine the effect of two putative key innovations, that is, the Crassulacean acid metabolism (CAM) and the water‐impounding tank, on speciation and extinction rates. To this aim, we develop a novel Bayesian implementation of the phylogenetic comparative method, binary state speciation and extinction, which enables hypotheses testing by Bayes factors and accommodates the uncertainty on model selection by Bayesian model averaging. Both CAM and tank habit were found to correlate with increased net diversification, thus fulfilling the criteria for key innovations. Our analyses further revealed that CAM photosynthesis is correlated with a twofold increase in speciation rate, whereas the evolution of the tank had primarily an effect on extinction rates that were found five times lower in tank‐forming lineages compared to tank‐less clades. These differences are discussed in the light of biogeography, ecology, and past climate change.