Elevated atmospheric CO2 affects soil microbial diversity associated with trembling aspen

The effects of elevated atmospheric CO₂ (560 p.p.m.) and subsequent plant responses on the soil microbial community composition associated with trembling aspen was assessed through the classification of 6996 complete ribosomal DNA sequences amplified from the Rhinelander WI free-air CO₂ and O₃ enrichment (FACE) experiments microbial community metagenome. This in-depth comparative analysis provides an unprecedented, detailed and deep branching profile of population changes incurred as a response to this environmental perturbation. Total bacterial and eukaryotic abundance does not change; however, an increase in heterotrophic decomposers and ectomycorrhizal fungi is observed. Nitrate reducers of the domain bacteria and archaea, of the phylum Crenarchaea , potentially implicated in ammonium oxidation, significantly decreased with elevated CO₂. These changes in soil biota are evidence for altered interactions between trembling aspen and the microorganisms in its surrounding soil, and support the theory that greater plant detritus production under elevated CO₂ significantly alters soil microbial community composition.     

Biomass and nutrients in tree root systems–sustainable harvesting of an intensively managed Pinus pinaster (Ait.) planted forest

To develop sources of renewable energy and to reduce greenhouse gas emissions, increasing attention has been given to the extraction of forest biomass, especially in the form of harvest residues. However, increasing the removal of biomass, and hence nutrients, has raised concerns about the sustainability of site fertility and forest productivity. The environmental cost of harvesting belowground biomass is still not fully understood. The objectives of this study were to (i) estimate the stocks of belowground biomass that potentially can be collected; (ii) measure the nutrient (N, P, K, Ca, Mg) concentrations of the different root compartments (stumps, coarse and thin roots); and to (iii) quantify the biomass and nutrient exports under different scenarios, including harvests of above and belowground compartments. The study was carried out on Pinus pinaster stands located in south‐western France. Results showed that roots could be a significant fuelwood resource, particularly at forest clear cutting. Negative relationships between root diameter and root nutrient concentration were observed, independently of root function or tree age. Such relationships can be used to accurately simulate nutrient concentrations in roots as well as nutrient exports. Combining our original results on roots with previously published data on the aboveground compartments showed that nutrient losses were higher in canopy harvest scenarios than in root harvest scenarios. This was mainly due to high nutrient concentrations of needles. We concluded that stump and root harvest could be sustainable in our study context, conversely to foliage harvest. Because thin roots have higher nutrient concentrations than coarse roots and the proportion of thin roots increased with an increase in the distance from the tree, collecting roots only in the close vicinity of the stumps should limit nutrient exports (particularly N) without unnecessarily reducing fuelwood biomass.     

Removal of BTEX compounds by industrial sludge microbes in batch systems: statistical analysis of main and interaction effects

Biodegradation is an effective technique to remediate polluted soil and groundwater. In the present experimental study, a mixed microbial culture obtained from the wastewater treatment sludge of a chemical industry was used to degrade liquid phase benzene, toluene, ethyl benzene, and xylene (BTEX), at individual initial concentrations varying between 15 and 75 mg/l. Experiments were conducted according to 2 ^k−1 fractional factorial design at the low (15 mg/l) and high (75 mg/l) levels of BTEX concentrations, to identify the main and interaction effects of parameters and their influence on biodegradation of individual BTEX compounds in mixtures. The individual removals varied between 16% and 75% when the concentrations of B, T, E, and X were sufficiently low in the mixture. However, both synergistic (removal of ethyl benzene) and antagonistic (removal of benzene) behavior were noticed when the concentrations of toluene and xylene was increased to higher levels. The individual removals were greater than 67% at their center point levels. The total BTEX removal values were later statistically analyzed and based on the Fischer’s variance ratio (F) and Probability values (P) it was observed that the main effects for total BTEX removal were significant than the squared and interaction effects.     

Antiviral Activity of TMC353121, a Respiratory Syncytial Virus (RSV) Fusion Inhibitor,in a Non-Human Primate Model

BackgroundThe study assessed the antiviral activity of TMC353121, a respiratory syncytial virus (RSV) fusion inhibitor, in a preclinical non-human primate challenge model with a viral shedding pattern similar to that seen in humans, following continuous infusion (CI).MethodsAfrican green monkeys were administered TMC353121 through CI, in 2 studies. Study 1 evaluated the prophylactic and therapeutic efficacy of TMC353121 at a target plasma level of 50 ng/mL (n=15; Group 1: prophylactic arm [Px50], 0.033 mg/mL TMC353121, flow rate 2.5 mL/kg/h from 24 hours pre-infection to 10 days; Group 2: therapeutic arm [Tx50], 0.033mg/mL TMC353121 from 24 hours postinfection to 8 days; Group 3: control [Vh1] vehicle, 24 hours post-infection to 8 days). Study 2 evaluated the prophylactic efficacy of TMC353121 at target plasma levels of 5 and 500 ng/mL (n=12; Group 1: prophylactic 5 arm [Px5], 0.0033 mg/mL TMC353121, flow rate 2.5 mL/kg/h from 72 hours pre-infection to 14 days; Group 2: prophylactic 500 arm [Px500], 0.33 mg/mL TMC353121; Group 3:control [Vh2] vehicle, 14 days). Bronchoalveolar lavage fluid and plasma were collected every 2 days from day 1 postinfection for pharmacokinetics and safety analysis.FindingsTMC353121 showed a dose-dependent antiviral activity, varying from 1log₁₀ reduction of peak viral load to complete inhibition of the RSV replication. Complete inhibition of RSV shedding was observed for a relatively low plasma exposure (0.39 μg/mL) and was associated with a dose-dependent reduction in INFγ, IL6 and MIP1α. TMC353121 administered as CI for 16 days was generally well-tolerated.ConclusionTMC353121 exerted dose-dependent antiviral effect ranging from full inhibition to absence of antiviral activity, in a preclinical model highly permissive for RSV replication. No new safety findings emerged from the study.     

中间偃麦草的GISH分析

以染色体组为E^eE^e的二倍体长穗偃麦草（Thinopyrum elongatum,2n=2x=14)、染色体组为E^bE^b的二倍体比萨偃麦草（Th.bessarabicum,2n=2x=14）、染色体组为StStStSt的四倍体拟鹅冠草（Pseudoroegneiria strigosa,2n=4x=28)的总基因组DNA为探针,对中间偃麦草（Th.intermedium)进行GISH分析。结果表明,中间偃麦草是由2个亲缘关系较近的染色体组、1个亲缘关系较远的染色体组构成;中间偃麦草所含的亲缘关系较近的染色体组分别与二倍长穗偃麦草染色体组E^e、比萨偃麦草染色体组E^b、以及1个亲缘关系较远的染色体组与拟鹅冠草染色体组St基本相似,但不完全一样,因此,中间偃麦草的染色体组用E^etE^etE^btStSt表示。     

Integrating the ‘genomic mosaic’ view of species into studies of biotic interactions: a comment on Bernhardsson et al. ()

The co‐occurrence of geographical structure in herbivore communities, metabolomes and defence genes in forest trees has been analysed in the context of ‘geographical mosaics’ of coevolution. A deeper understanding of these important issues will require full integration of a ‘genomic mosaic’ view of species into community ecology.     

Y-STR diversity and sex-biased gene flow among Caribbean populations

In the present study, we report, for the first time, the allele and haplotype frequencies of 17 Y-STR (Y-filer) loci in the populations of Haiti, Jamaica and the Bahamas (Abaco, Eleuthera, Exuma, Grand Bahama, Long Island and New Providence). This investigation was undertaken to assess the paternal genetic structure of the abovementioned Caribbean islands. A total of 607 different haplotypes were identified among the 691 males examined, of which 537 (88.5%) were unique. Haplotype diversities (HD) ranged from 0.989 in Long Island to 1.000 in Grand Bahama, with limited haplotype sharing observed among these Caribbean collections. Discriminatory capacity (DC) values were also high, ranging from 79.1% to 100% in Long Island and Grand Bahama, respectively, illustrating the capacity of this set of markers to differentiate between patrilineal related individuals within each population. Phylogenetic comparison of the Bahamian, Haitian and Jamaican groups with available African, European, East Asian and Native American populations reveals strong genetic ties with the continental African collections, a finding that corroborates our earlier work using autosomal STR and Y-chromosome binary markers. In addition, various degrees of sex-biased gene flow exhibiting disproportionately higher European paternal (as compared to autosomal) influences were detected in all Caribbean islands genotyped except for Abaco and Eleuthera. We attribute the presence or absence of asymmetric gene flow to unique, island specific demographic events and family structures.     

Mutations in LRRC50 Predispose Zebrafish and Humans to Seminomas

Seminoma is a subclass of human testicular germ cell tumors (TGCT), the most frequently observed cancer in young men with a rising incidence. Here we describe the identification of a novel gene predisposing specifically to seminoma formation in a vertebrate model organism. Zebrafish carrying a heterozygous nonsense mutation in Leucine-Rich Repeat Containing protein 50 (lrrc50 also called dnaaf1), associated previously with ciliary function, are found to be highly susceptible to the formation of seminomas. Genotyping of these zebrafish tumors shows loss of heterozygosity (LOH) of the wild-type lrrc50 allele in 44.4% of tumor samples, correlating with tumor progression. In humans we identified heterozygous germline LRRC50 mutations in two different pedigrees with a family history of seminomas, resulting in a nonsense Arg488* change and a missense Thr590Met change, which show reduced expression of the wild-type allele in seminomas. Zebrafish in vivo complementation studies indicate the Thr590Met to be a loss-of-function mutation. Moreover, we show that a pathogenic Gln307Glu change is significantly enriched in individuals with seminoma tumors (13% of our cohort). Together, our study introduces an animal model for seminoma and suggests LRRC50 to be a novel tumor suppressor implicated in human seminoma pathogenesis.     

Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling

Signaling pathways are characterized by crosstalk, feedback and feedforward mechanisms giving rise to highly complex and cell-context specific signaling networks. Dissecting the underlying relations is crucial to predict the impact of targeted perturbations. However, a major challenge in identifying cell-context specific signaling networks is the enormous number of potentially possible interactions. Here, we report a novel hybrid mathematical modeling strategy to systematically unravel hepatocyte growth factor (HGF) stimulated phosphoinositide-3-kinase (PI3K) and mitogen activated protein kinase (MAPK) signaling, which critically contribute to liver regeneration. By combining time-resolved quantitative experimental data generated in primary mouse hepatocytes with interaction graph and ordinary differential equation modeling, we identify and experimentally validate a network structure that represents the experimental data best and indicates specific crosstalk mechanisms. Whereas the identified network is robust against single perturbations, combinatorial inhibition strategies are predicted that result in strong reduction of Akt and ERK activation. Thus, by capitalizing on the advantages of the two modeling approaches, we reduce the high combinatorial complexity and identify cell-context specific signaling networks.