Comparison of Three Products Based on Phlebiopsis gigantea for the Control of Heterobasidion annosum in Europe

The fungus Phlebiopsis gigantea has been used in Europe as a biological agent for the control of conifer root and butt (caused by Heterobasidion annosum ) for nearly 40 years. P. gigantea competes with H. annosum for the woody resource within conifer stumps, and is applied to stump surfaces at felling. Three distinct biological control products based on P. gigantea have been developed: PG Suspension in the UK, PG IBL in Poland and Rotstop in Finland. The formulations are of oidia, which are maintained in a sucrose suspension, sawdust, or a wettable powder, respectively. PG Suspension and PG IBL are applied to pine stumps, while Rotstop is equally as effective on pine as on Norway spruce stumps. For each product, isolates of P. gigantea are selected from the wild and are screened for their competitive ability against H. annosum before formulation. Viability and purity checks are undertaken throughout the production cycle and during routine use. The increasing use of mechanized harvesting machines to fell and process trees is having an impact on this biological control system, the formulations having to be compatible with the mechanical application systems and vice versa. This paper compares the formulation, testing and application of the three products, and considers some aspects of their future development.     

Inoculation of willows (Salix spp.) with ectomycorrhizal fungi on mined boreal peatland

Inoculation with ectomycorrhizal fungi was explored as a means to improve productivity of experimental short-rotation plantations of the willowsSalix viminalis andSalix dasyclados for biomass production on surface-mined peatlands in northern Finland. Both willow species formed ectomycorrhizas withAmanita spp.,Cortinarius purpurascens, Entoloma nidorosum, otherEntoloma spp.,Hebeloma crustuliniforme, H. pusillum, Laccaria bicolor, andPaxillus involutus in greenhouse experiments.Field trials on a mined peatland site revealed (after one growing season) statistically significant growth stimulation after inoculation due to mycorrhiza formation in both willow species: plants inoculated withEntoloma were sometimes twice as large as control plants. However, such effects were observed only in plots receiving normal phosphate fertilization as opposed to low phosphate application, and were not consistent from season to season. With the inoculum of other species (Cortinarius, Hebeloma andPaxillus) some evidence of growth enhancement was found in the field, but these results were sometimes attributable to non-symbiotic effects of inoculation.     

Impact of calcific aortic valve disease on valve mechanics

Biomechanics and Modeling in Mechanobiology - The aortic valve is a highly dynamic structure characterized by a transvalvular flow that is unsteady, pulsatile, and characterized by episodes of...     

Ranking non-synonymous single nucleotide polymorphisms based on disease concepts

As the number of non-synonymous single nucleotide polymorphisms (nsSNPs) identified through whole-exome/whole-genome sequencing programs increases, researchers and clinicians are becoming increasingly reliant upon computational prediction algorithms designed to prioritize potential functional variants for further study. A large proportion of existing prediction algorithms are ‘disease agnostic’ but are nevertheless quite capable of predicting when a mutation is likely to be deleterious. However, most clinical and research applications of these algorithms relate to specific diseases and would therefore benefit from an approach that discriminates between functional variants specifically related to that disease from those which are not. In a whole-exome/whole-genome sequencing context, such an approach could substantially reduce the number of false positive candidate mutations. Here, we test this postulate by incorporating a disease-specific weighting scheme into the Functional Analysis through Hidden Markov Models (FATHMM) algorithm. When compared to traditional prediction algorithms, we observed an overall reduction in the number of false positives identified using a disease-specific approach to functional prediction across 17 distinct disease concepts/categories. Our results illustrate the potential benefits of making disease-specific predictions when prioritizing candidate variants in relation to specific diseases. A web-based implementation of our algorithm is available at http://fathmm.biocompute.org.uk.     

Single gene enables plant pathogenic Pectobacterium to overcome host-specific chemical defence

Plants of the Brassicales order, including Arabidopsis and many common vegetables, produce toxic isothiocyanates to defend themselves against pathogens. Despite this defence, plant pathogenic microorganisms like Pectobacterium cause large yield losses in fields and during storage of crops. The bacterial gene saxA was previously found to encode isothiocyanate hydrolase that degrades isothiocyanates in vitro. Here we demonstrate in planta that saxA is a virulence factor that can overcome the chemical defence system of Brassicales plants. Analysis of the distribution of saxA genes in Pectobacterium suggests that saxA from three different phylogenetic origins are present within this genus. Deletion of saxA genes representing two of the most common classes from P. odoriferum and P. versatile resulted in significantly reduced virulence on Arabidopsis thaliana and Brassica oleracea. Furthermore, expressing saxA from a plasmid in a potato-specific P. parmentieri strain that does not naturally harbour this gene significantly increased the ability of the strain to macerate Arabidopsis. These findings suggest that a single gene may have a significant role in defining the host range of a plant pathogen.     

Serum amyloid A activates the NLRP3 inflammasome via P2X7 receptor and a cathepsin B-sensitive pathway

Serum amyloid A (SAA) is an acute-phase protein, the serum levels of which can increase up to 1000-fold during inflammation. SAA has a pathogenic role in amyloid A-type amyloidosis, and increased serum levels of SAA correlate with the risk for cardiovascular diseases. IL-1β is a key proinflammatory cytokine, and its secretion is strictly controlled by the inflammasomes. We studied the role of SAA in the regulation of IL-1β production and activation of the inflammasome cascade in human and mouse macrophages, as well as in THP-1 cells. SAA could provide a signal for the induction of pro-IL-1β expression and for inflammasome activation, resulting in secretion of mature IL-1β. Blocking TLR2 and TLR4 attenuated SAA-induced expression of IL1B, whereas inhibition of caspase-1 and the ATP receptor P2X(7) abrogated the release of mature IL-1β. NLRP3 inflammasome consists of the NLRP3 receptor and the adaptor protein apoptosis-associated speck-like protein containing CARD (a caspase-recruitment domain) (ASC). SAA-mediated IL-1β secretion was markedly reduced in ASC(-/-) macrophages, and silencing NLRP3 decreased IL-1β secretion, confirming NLRP3 as the SAA-responsive inflammasome. Inflammasome activation was dependent on cathepsin B activity, but it was not associated with lysosomal destabilization. SAA also induced secretion of cathepsin B and ASC. In conclusion, SAA can induce the expression of pro-IL-1β and activation of the NLRP3 inflammasome via P2X(7) receptor and a cathepsin B-sensitive pathway. Thus, during systemic inflammation, SAA may promote the production of IL-1β in tissues. Furthermore, the SAA-induced secretion of active cathepsin B may lead to extracellular processing of SAA and, thus, potentially to the development of amyloid A amyloidosis.     

Home range,survival, and dispersal of endangered Saimaa ringed seal pups: Implications for conservation

Lake Saimaa in eastern Finland is inhabited by a critically endangered ringed seal subspecies Pusa hispida saimensis. Since accidental mortality in gill nets, resulting in reduced pup survival, is considered to be the main factor contributing to the decline in its population, fishing restriction areas have been established. In this study, 10 pups were located daily using very high frequency (VHF) telemetry to estimate their home ranges, movements, and survival. The pups dispersed after weaning at the age of ca. 3 mo and moved up to 15 km a day between consecutive locations and up to 25 km away from their birth sites. The home ranges of the pups at the age of 3–4 mo were variable in size, from 3 to 162 km². The pups preferred the same shallow water areas (<6 m) that were used for gill net fishing. The annual fishing restrictions covered an average of 83% of the pups’ home ranges. Four of the pups were nevertheless killed in fishing gear. The results have implications for Saimaa ringed seal management and conservation. For instance, large home ranges of pups and the long distances movements should be taken into account when zoning shore use and imposing fishing restrictions.     

The impact of crop plant cultivation and peat amendment on soil microbial activity and structure

A rapid means for restoring soil fertility could be addition of peat to the plough layer. The impact of cultivation of eight different crops (the joint impact of plant and the management tailored for each plant), with and without soil amendment by peat treatment on soil microbiological, physical and chemical properties was assessed for two consecutive growing seasons. As a measure of the functional diversity of soil microbial community we estimated the activity of several different extracellular soil enzymes using the ZymProfiler® test kit. ATP content was measured to yield information on the amount of the active microbial biomass, and phospholipid fatty acid (PLFA) profiles were analysed to reveal the microbial community structure. The enzyme activity patterns of the soil samples indicated several differences due to the different crops and years but ATP content and PLFA profiles were rather stable. However, microbial biomass as total amount of PLFAs depended on the plant and peat treatment and ATP content varied between the years. The effects of the peat treatments were less clearly indicated by the biological parameters one or two years after the amendment, as only arylsulphatase and β-xylosidase activities were affected in both the years. Soil moisture, affecting enzyme activities, depended on the year and crop plant and peat addition increased it. Abbreviations: AMC – 7-amino-4-methylcoumarin; AP – aminopeptidase; ATP – adenosine triphosphate; C_mic– microbial biomass carbon; DNA – deoxyribonucleic acid; EC – electrical conductivity; FAME – fatty acid methyl ester; fw – fresh weight; MUF – 4-methylumbelliferyl; na – not added; N_mic– microbial biomass nitrogen; PDE – phosphodiesterase; PLFA – phospholipid fatty acid; PME – phosphomonoesterase; SOM – soil organic matter     

RMBNToolbox: random models for biochemical networks

Background  

There is an increasing interest to model biochemical and cell biological networks, as well as to the computational analysis of these models. The development of analysis methodologies and related software is rapid in the field. However, the number of available models is still relatively small and the model sizes remain limited. The lack of kinetic information is usually the limiting factor for the construction of detailed simulation models.