Analysis of the genome of Spodoptera frugiperda nucleopolyhedrovirus (SfMNPV-19) and of the high genomic heterogeneity in group II nucleopolyhedroviruses

The genome of the most virulent among 22 Brazilian geographical isolates of Spodoptera frugiperda nucleopolyhedrovirus, isolate 19 (SfMNPV-1 9), was completely sequenced and shown to comprise 132 565 bp and 141 open reading frames (ORFs). A total of 11 ORFs with no homology to genes in the GenBank database were found. Of those, four had typical baculovirus; promoter motifs and polyadenylation sites. Computer-simulated restriction enzyme cleavage patterns of SfMNPV-1 9 were compared with published physical maps of other SfMNPV isolates. Differences were observed in terms of the restriction profiles and genome size. Comparison of SfMNPV-1 9 with the sequence of the SfMNPV isolate 3AP2 indicated that they differed due to a 1427 bp deletion, as well as by a series of smaller deletions and point mutations. The majority of genes of SfMNPV-1 9 were conserved in the closely related Spodoptera exigua NPV (SeMNPV) and Agrotis segetum NPV (AgseMNPV-A), but a few regions experienced major changes and rearrangements. Synthenic maps for the genomes of group 11 NPVs revealed that gene collinearity was observed only within certain clusters. Analysis of the dynamics of gene gain and loss along the phylogenetic tree of the NPVs showed that group 11 had only five defining genes and supported the hypothesis that these viruses form ten highly divergent ancient lineages. Crucially, more than 60% of the gene gain events followed a power-law relation to genetic distance among baculoviruses, indicative of temporal organization in the gene accretion process.

MuRF1 is a muscle fiber-type II associated factor and together with MuRF2 regulates type-II fiber trophicity and maintenance

MuRF1 is a member of the RBCC (RING, B-box, coiled-coil) superfamily that has been proposed to act as an atrogin during muscle wasting. Here, we show that MuRF1 is preferentially induced in type-II muscle fibers after denervation. Fourteen days after denervation, MuRF1 protein was further elevated but remained preferentially expressed in type-II muscle fibers. Consistent with a fiber-type dependent function of MuRF1, the tibialis anterior muscle (rich in type-II muscle fibers) was considerably more protected in MuRF1-KO mice from muscle wasting when compared to soleus muscle with mixed fiber-types. We also determined fiber-type distributions in MuRF1/MuRF2 double-deficient KO (dKO) mice, because MuRF2 is a close homolog of MuRF1. MuRF1/MuRF2 dKO mice showed a profound loss of type-II fibers in soleus muscle. As a potential mechanism we identified the interaction of MuRF1/MuRF2 with myozenin-1, a calcineurin/NFAT regulator and a factor required for maintenance of type-II muscle fibers. MuRF1/MuRF2 dKO mice had lost myozenin-1 expression in tibialis anterior muscle, implicating MuRF1/MuRF2 as regulators of the calcineurin/NFAT pathway. In summary, our data suggest that expression of MuRF1 is required for remodeling of type-II fibers under pathophysiological stress states, whereas MuRF1 and MuRF2 together are required for maintenance of type-II fibers, possibly via the regulation of myozenin-1. (C) 2010 Elsevier Inc. All rights reserved.

Thermochronology of central Ribeira Fold Belt, SE Brazil: Petrological and geochronological evidence for long-term high temperature maintenance during Western Gondwana amalgamation

The studied sector of the central Ribeira Fold Belt (SE Brazil) comprises metatexites, diatexites, charnockites and blastomylonites. This study integrates petrological and thermochronological data in order to constrain the thermotectonic and geodynamic evolution of this Neoproterozoic-Ordovician mobile belt during Western Gondwana amalgamation. New data indicate that after an earlier collision stage at similar to 610 Ma (zircon, U-Pb age), peak metamorphism and lower crust partial melting, coeval with the main regional high grade D(1) thrust deformation, occurred at 572-562 Ma (zircon, U-Pb ages). The overall average cooling rate was low (<5 degrees C/Ma) from 750 to 250 degrees C (at similar to 455 Ma; biotite-WR Rb-Sr age), but disparate cooling paths indicate differential uplift between distinct lithotypes: (a) metatexites and blastomylonites show a overall stable 3-5 degrees C/Ma cooling rate; (b) charnockites and associated rocks remained at T>650 degrees C during sub-horizontal D(2) shearing until similar to 510-470 Ma (garnet-WR Sm-Nd ages) (1-2 degrees C/Ma), being then rapidly exhumed/cooled (8-30 degrees C/Ma) during post-orogenic D(3) deformation with late granite emplacement at similar to 490 Ma (zircon, U-Pb age). Cooling rates based on garnet-biotite Fe-Mg diffusion are broadly consistent with the geochronological cooling rates: (a) metatexites were cooled faster at high temperatures (6 degrees C/Ma) and slowly at low temperatures (0.1 degrees C/Ma), decreasing cooling rates with time; (b) charnockites show low cooling rates (2 degrees C/Ma) near metamorphic peak conditions and high cooling rates (120 degrees C/Ma) at lower temperatures, increasing cooling rates during retrogression. The charnockite thermal evolution and the extensive production of granitoid melts in the area imply that high geothermal gradients were sustained fora long period of time (50-90 Ma). This thermal anomaly most likely reflects upwelling of asthenospheric mantle and magma underplating coupled with long-term generation of high HPE (heat producing elements) granitoids. These factors must have sustained elevated crustal geotherms for similar to 100 Ma, promoting widespread charnockite generation at middle to lower crustal levels. (C) 2010 Elsevier B.V. All rights reserved.

Software maintenance project delays prediction using Bayesian Networks

Managing software maintenance is rarely a precise task due to uncertainties concerned with resources and services descriptions. Even when a well-established maintenance process is followed, the risk of delaying tasks remains if the new services are not precisely described or when resources change during process execution. Also, the delay of a task at an early process stage may represent a different delay at the end of the process, depending on complexity or services reliability requirements. This paper presents a knowledge-based representation (Bayesian Networks) for maintenance project delays based on specialists experience and a corresponding tool to help in managing software maintenance projects. (c) 2006 Elsevier Ltd. All rights reserved.

Superoxide Dismutase 1-mediated Production of Ethanol- and DNA-derived Radicals in Yeasts Challenged with Hydrogen Peroxide MOLECULAR INSIGHTS INTO THE GENOME INSTABILITY OF PEROXIREDOXIN-NULL STRAINS

Peroxiredoxins are receiving increasing attention as defenders against oxidative damage and sensors of hydrogen peroxide-mediated signaling events. In the yeast Saccharomyces cerevisiae, deletion of one or more isoforms of the peroxiredoxins is not lethal but compromises genome stability by mechanisms that remain under scrutiny. Here, we show that cytosolic peroxiredoxin-null cells (tsa1 Delta tsa2 Delta) are more resistant to hydrogen peroxide than wildtype (WT) cells and consume it faster under fermentative conditions. Also, tsa1 Delta tsa2 Delta cells produced higher yields of the 1-hydroxyethyl radical from oxidation of the glucose metabolite ethanol, as proved by spin-trapping experiments. A major role for Fenton chemistry in radical formation was excluded by comparing WT and tsa1 Delta tsa2 Delta cells with respect to their levels of total and chelatable metal ions and of radical produced in the presence of chelators. The main route for 1-hydroxyethyl radical formation was ascribed to the peroxidase activity of Cu, Zn-superoxide dismutase (Sod1), whose expression and activity increased similar to 5- and 2-fold, respectively, in tsa1 Delta tsa2 Delta compared with WT cells. Accordingly, overexpression of human Sod1 in WT yeasts led to increased 1-hydroxyethyl radical production. Relevantly, tsa1 Delta tsa2 Delta cells challenged with hydrogen peroxide contained higher levels of DNA-derived radicals and adducts as monitored by immuno-spin trapping and incorporation of (14)C from glucose into DNA, respectively. The results indicate that part of hydrogen peroxide consumption by tsa1 Delta tsa2 Delta cells is mediated by induced Sod1, which oxidizes ethanol to the 1-hydroxyethyl radical, which, in turn, leads to increased DNA damage. Overall, our studies provide a pathway to account for the hypermutability of peroxiredoxin-null strains.

Improved Road Design for Future Maintenance - Analysis of Road Barrier Repair Costs

The cost of a road construction over its service life is a function of the design, quality of construction, maintenance strategies and maintenance operations. Unfortunately, designers often neglect a very important aspect which is the possibility to perform future maintenance activities. The focus is mainly on other aspects such as investment costs, traffic safety, aesthetic appearance, regional development and environmental effects. This licentiate thesis is a part of a Ph.D. project entitled “Road Design for lower maintenance costs” that aims to examine how the life-cycle costs can be optimized by selection of appropriate geometrical designs for the roads and their components. The result is expected to give a basis for a new method used in the road planning and design process using life-cycle cost analysis with particular emphasis on road maintenance. The project started with a review of literature with the intention to study conditions causing increased needs for road maintenance, the efforts made by the road authorities to satisfy those needs and the improvement potential by consideration of maintenance aspects during planning and design. An investigation was carried out to identify the problems which obstruct due consideration of maintenance aspects during the road planning and design process. This investigation focused mainly on the road planning and design process at the Swedish Road Administration. However, the road planning and design process in Denmark, Finland and Norway were also roughly evaluated to gain a broader knowledge about the research subject. The investigation was carried out in two phases: data collection and data analysis. Data was collected by semi-structured interviews with expert actors involved in planning, design and maintenance and by a review of design-related documents. Data analyses were carried out using a method called “Change Analysis”. This investigation revealed a complex combination of problems which result in inadequate consideration of maintenance aspects. Several urgent needs for changes to eliminate these problems were identified. Another study was carried out to develop a model for calculation of the repair costs for damages of different road barrier types and to analyse how factors such as road type, speed limits, barrier types, barrier placement, type of road section, alignment and seasonal effects affect the barrier damages and the associated repair costs. This study was carried out using a method called the “Case Study Research Method”. Data was collected from 1087 barrier repairs in two regional offices of the Swedish Road Administration, the Central Region and the Western Region. A table was established for both regions containing the repair cost per vehicle kilometre for different combinations of barrier types, road types and speed limits. This table can be used by the designers in the calculation of the life-cycle costs for different road barrier types.

Road Design for Future Maintenance : Life-cycle Cost Analyses for Road Barriers

The cost of a road construction over its service life is a function of design, quality of construction as well as maintenance strategies and operations. An optimal life-cycle cost for a road requires evaluations of the above mentioned components. Unfortunately, road designers often neglect a very important aspect, namely, the possibility to perform future maintenance activities. Focus is mainly directed towards other aspects such as investment costs, traffic safety, aesthetic appearance, regional development and environmental effects. This doctoral thesis presents the results of a research project aimed to increase consideration of road maintenance aspects in the planning and design process. The following subgoals were established: Identify the obstacles that prevent adequate consideration of future maintenance during the road planning and design process; and Examine optimisation of life-cycle costs as an approach towards increased efficiency during the road planning and design process. The research project started with a literature review aimed at evaluating the extent to which maintenance aspects are considered during road planning and design as an improvement potential for maintenance efficiency. Efforts made by road authorities to increase efficiency, especially maintenance efficiency, were evaluated. The results indicated that all the evaluated efforts had one thing in common, namely ignorance of the interrelationship between geometrical road design and maintenance as an effective tool to increase maintenance efficiency. Focus has mainly been on improving operating practises and maintenance procedures. This fact might also explain why some efforts to increase maintenance efficiency have been less successful. An investigation was conducted to identify the problems and difficulties, which obstruct due consideration of maintainability during the road planning and design process. A method called “Change Analysis” was used to analyse data collected during interviews with experts in road design and maintenance. The study indicated a complex combination of problems which result in inadequate consideration of maintenance aspects when planning and designing roads. The identified problems were classified into six categories: insufficient consulting, insufficient knowledge, regulations and specifications without consideration of maintenance aspects, insufficient planning and design activities, inadequate organisation and demands from other authorities. Several urgent needs for changes to eliminate these problems were identified. One of the problems identified in the above mentioned study as an obstacle for due consideration of maintenance aspects during road design was the absence of a model for calculating life-cycle costs for roads. Because of this lack of knowledge, the research project focused on implementing a new approach for calculating and analysing life-cycle costs for roads with emphasis on the relationship between road design and road maintainability. Road barriers were chosen as an example. The ambition is to develop this approach to cover other road components at a later stage. A study was conducted to quantify repair rates for barriers and associated repair costs as one of the major maintenance costs for road barriers. A method called “Case Study Research Method” was used to analyse the effect of several factors on barrier repairs costs, such as barrier type, road type, posted speed and seasonal effect. The analyses were based on documented data associated with 1625 repairs conducted in four different geographical regions in Sweden during 2006. A model for calculation of average repair costs per vehicle kilometres was created. Significant differences in the barrier repair costs were found between the studied barrier types. In another study, the injuries associated with road barrier collisions and the corresponding influencing factors were analysed. The analyses in this study were based on documented data from actual barrier collisions between 2005 and 2008 in Sweden. The result was used to calculate the cost for injuries associated with barrier collisions as a part of the socio-economic cost for road barriers. The results showed significant differences in the number of injuries associated with collisions with different barrier types. To calculate and analyse life-cycle costs for road barriers a new approach was developed based on a method called “Activity-based Life-cycle Costing”. By modelling uncertainties, the presented approach gives a possibility to identify and analyse factors crucial for optimising life-cycle costs. The study showed a great potential to increase road maintenance efficiency through road design. It also showed that road components with low investment costs might not be the best choice when including maintenance and socio-economic aspects. The difficulties and problems faced during the collection of data for calculating life-cycle costs for road barriers indicated a great need for improving current data collecting and archiving procedures. The research focused on Swedish road planning and design. However, the conclusions can be applied to other Nordic countries, where weather conditions and road design practices are similar. The general methodological approaches used in this research project may be applied also to other studies.

Monitoring vegetation on railway embankments : supporting maintenance decisions

The national railway administrations in Scandinavia, Germany, and Austria mainly resort to manual inspections to control vegetation growth along railway embankments. Manually inspecting railways is slow and time consuming. A more worrying aspect concerns the fact that human observers are often unable to estimate the true cover of vegetation on railway embankments. Further human observers often tend to disagree with each other when more than one observer is engaged for inspection. Lack of proper techniques to identify the true cover of vegetation even result in the excess usage of herbicides; seriously harming the environment and threating the ecology. Hence work in this study has investigated aspects relevant to human variationand agreement to be able to report better inspection routines. This was studied by mainly carrying out two separate yet relevant investigations.First, thirteen observers were separately asked to estimate the vegetation cover in nine imagesacquired (in nadir view) over the railway tracks. All such estimates were compared relatively and an analysis of variance resulted in a significant difference on the observers’ cover estimates (p<0.05). Bearing in difference between the observers, a second follow-up field-study on the railway tracks was initiated and properly investigated. Two railway segments (strata) representingdifferent levels of vegetationwere carefully selected. Five sample plots (each covering an area of one-by-one meter) were randomizedfrom each stratumalong the rails from the aforementioned segments and ten images were acquired in nadir view. Further three observers (with knowledge in the railway maintenance domain) were separately asked to estimate the plant cover by visually examining theplots. Again an analysis of variance resulted in a significant difference on the observers’ cover estimates (p<0.05) confirming the result from the first investigation.The differences in observations are compared against a computer vision algorithm which detects the "true" cover of vegetation in a given image. The true cover is defined as the amount of greenish pixels in each image as detected by the computer vision algorithm. Results achieved through comparison strongly indicate that inconsistency is prevalent among the estimates reported by the observers. Hence, an automated approach reporting the use of computer vision is suggested, thus transferring the manual inspections into objective monitored inspections

Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait

Understanding the genetic basis of traits involved in adaptation is a major challenge in evolutionary biology but remains poorly understood. Here, we use genome-wide association mapping using a custom 50 k single nucleotide polymorphism (SNP) array in a natural population of collared flycatchers to examine the genetic basis of clutch size, an important life-history trait in many animal species. We found evidence for an association on chromosome 18 where one SNP significant at the genome-wide level explained 3.9% of the phenotypic variance. We also detected two suggestive quantitative trait loci (QTLs) on chromosomes 9 and 26. Fitness differences among genotypes were generally weak and not significant, although there was some indication of a sex-by-genotype interaction for lifetime reproductive success at the suggestive QTL on chromosome 26. This implies that sexual antagonism may play a role in maintaining genetic variation at this QTL. Our findings provide candidate regions for a classic avian life-history trait that will be useful for future studies examining the molecular and cellular function of, as well as evolutionary mechanisms operating at, these loci.