UCE: A uracil excision (USER™)-based toolbox for transformation of cereals

Background  

Cloning of gene casettes and other DNA sequences into the conventional vectors for biolistic or Agrobacterium-mediated transformation is hampered by a limited amount of unique restriction sites and by the difficulties often encountered when ligating small single strand DNA overhangs. These problems are obviated by "The Uracil Specific Excision Reagent (USER™)" technology (New England Biolabs) which thus offers a new and very time-efficient method for engineering of big and complex plasmids.     

The landscape matrix modifies the effect of habitat fragmentation in grassland butterflies

The landscape matrix is suggested to influence the effect of habitat fragmentation on species richness, but the generality of this prediction has not been tested. Here, we used data from 10 independent studies on butterfly species richness, where the matrix surrounding grassland patches was dominated by either forest or arable land to test if matrix land use influenced the response of species richness to patch area and connectivity. To account for the possibility that some of the observed species use the matrix as their main or complementary habitat, we analysed the effects on total species richness and on the richness of grassland specialist and non-specialist (generalists and specialists on other habitat types) butterflies separately. Specialists and non-specialists were defined separately for each dataset. Total species richness and the richness of grassland specialist butterflies were positively related to patch area and forest cover in the matrix, and negatively to patch isolation. The strength of the species-area relationship was modified by matrix land use and had a slope that decreased with increasing forest cover in the matrix. Potential mechanisms for the weaker effect of grassland fragmentation in forest-dominated landscapes are (1) that the forest matrix is more heterogeneous and contains more resources, (2) that small grassland patches in a matrix dominated by arable land suffer more from negative edge effects or (3) that the arable matrix constitutes a stronger barrier to dispersal between populations. Regardless of the mechanisms, our results show that there are general effects of matrix land use across landscapes and regions, and that landscape management that increases matrix quality can be a complement to habitat restoration and re-creation in fragmented landscapes.     

Associations between use,activities and characteristics of the outdoor environment at workplaces

Today, office work in western societies is more sedentary and more mentally demanding than ever before. This way of working plays a role in the increase in lifestyle diseases related to sedentary routines and stress. Green outdoor environments have been found to motivate physical activity and reduce stress levels. In this study, we therefore considered these environments to have a positive affect on work force health and wellbeing. However, research on the workplace outdoor environment is still limited. To investigate how and why the workplace outdoor environment is used by office workers and the impact of these environments on office workers’ health and wellbeing, five research questions were formulated. The questions addressed the use of the outdoor environments; the outdoor activities; encouragement and impediments for going outdoors; characteristics of the outdoor environment, and the impact of workplace outdoor environments on employees’ health, job satisfaction and work performance. In order to answer these research questions, we conducted a web-based questionnaire, completed by (N) 402 office workers from six Danish companies. The results show that 37.8% of the respondents spent time outdoors during their working day, and that the proportion of men spending time outdoors was higher than the proportion of women. Eight outdoor activities were identified, and significant relationships between the outdoor activities and perceived sensory dimensions (PSD) of the outdoor environment were found, indicating that the presence of the dimension ‘serene’ increased the odds for respondents going outdoors and that five of the eight activities would be performed. Only few significant relationships between outdoor environment use and employee health, job satisfaction and work performance were identified.     

Entry of adult Atlantic salmon into a tributary of the Aberdeenshire Dee,Scotland

Upstream counts of adult salmon in a tributary to the River Dee during autumn and winter were examined over a 13‐year period using an optical fish counter. Statistical analysis indicated that salmon were mainly primed to enter the tributary at a particular time of year, peaking at early December. However, environmental factors also had a large influence. Entry of salmon was initiated by high flow rates in the main stem of the River Dee. Increases in water level in the tributary itself were not needed to stimulate the entry of salmon. Moreover, a change in flow from 1 day to the next did not result in a response from salmon. Rather, they reacted only after more than a day of flow increase. There was no consistent threshold level of flow that triggered tributary entry. The upstream passage of salmon was reduced at low temperatures (below 3°C). The numbers of salmon migrating upstream showed a gradual increase as the temperatures increased up to 11°C, and then sharply decreased at higher temperatures. Female salmon migrated earlier by about 2 weeks on average than males. Increasingly, counters and traps are being installed on spawning tributaries to examine the state of salmon stocks. Caution should be exercised, however, in using upstream entry data from individual tributaries to provide an overall assessment of salmon abundance, as local conditions in the tributaries may affect the salmon counts in particular years.     

Real-time RT-qPCR assay to detect sequences in the Piscine orthoreovirus-1 genome segment S1 associated with heart and skeletal muscle inflammation in Atlantic salmon

During the last decade, Piscine orthoreovirus was identified as the main causative agent of heart and skeletal muscle inflammation (HSMI) in Atlantic Salmon, Norway. A recent study showed that PRV-1 sequences from salmonid collected in North Atlantic Pacific Coast (NAPC) grouped separately from the Norwegian sequences found in Atlantic Salmon diagnosed with HSMI. Currently, the routine assay used to screen for PRV-1 in NAPC water and worldwide cannot differentiate between the two groups of PRV-1. Therefore, this study aimed at developing a real-time polymerase chain reaction (RT-qPCR) assay to target the PRV-1 genome segments specific for variants associated with HSMI. The assay was optimized and tested against 71 tissue samples collected from different regions including Norway, Chile and both coast of Canada and different hosts farmed Atlantic Salmon, wild Coho Salmon and escaped Atlantic Salmon collected in British Columbia, West Coast of Canada. This assay has the potential to be used for screening salmonids and non-salmonids that may carry PRV-1 potentially causing HSMI.     

Distribution of RTX toxin genes in strains of [Actinobacillus] rossii and [Pasteurella] mairii

Strains of [Actinobacillus] rossii, [Pasteurella] mairii and [Pasteurella] aerogenes can be isolated from abortion in swine. The RTX toxin Pax has previously been found only in those [P.] aerogenes strains isolated from abortion. Nothing is known about RTX toxins in field isolates of the other two species. To gain insight into the distribution of selected RTX toxin genes and their association with abortion, PCR screening for the pax, apxII and apxIII operons on 21 [A.] rossii and seven [P.] mairii isolates was done. Since species can be phenotypically misidentified, the study was backed up by a phylogenetic analysis of all strains based on 16S rRNA, rpoB and infB genes. The pax gene was detected in all [P.] mairii but not in [A.] rossii strains. No apx genes were found in [P.] mairii but different gene combinations for apx were detected in [A.] rossii strains. Most of these strains were positive for apxIII, either alone or in combination with apxII. Whereas pax was found to be associated to strains from abortion no such indication could be found with apx in [A.] rossii strains. Phylogenetically [A.] rossii strains formed a heterogeneous cluster separated from Actinobacillus sensu stricto. [P.] mairii strains clustered with [P.] aerogenes but forming a separate branch. The fact that [P.] aerogenes, [P.] mairii and [A.] rossii can phylogenetically clearly be identified and might contain distinct RTX toxin genes allows their proper diagnosis and will further help to investigate their role as pathogens.     

Extensive gene traffic on the mammalian X chromosome

Mammalian sex chromosomes have undergone profound changes since evolving from ancestral autosomes. By examining retroposed genes in the human and mouse genomes, we demonstrate that, during evolution, the mammalian X chromosome has generated and recruited a disproportionately high number of functional retroposed genes, whereas the autosomes experienced lower gene turnover. Most autosomal copies originating from X-linked genes exhibited testis-biased expression. Such export is incompatible with mutational bias and is likely driven by natural selection to attain male germline function. However, the excess recruitment is consistent with a combination of both natural selection and mutational bias.     

Growth performance,nutrient digestibility and intestinal morphology of rainbow trout (Oncorhynchus mykiss) fed graded levels of the yeasts Saccharomyces cerevisiae and Wickerhamomyces anomalus

In a 10‐week study, we evaluated the effects of replacing 20%, 40% or 60% of fishmeal (present in control diet at 300 g/kg) on a digestible protein basis with yeast Saccharomyces cerevisiae or a yeast mixture of Wickerhamomyces anomalus and S. cerevisiae on growth performance, nutrient digestibility, nutrient retention and intestinal health of rainbow trout (Oncorhynchus mykiss). Triplicate tanks with 35 rainbow trout (144.7 ± 25.1 g mean ± SEM) were fed rations of 1.5% of total biomass per tank. Replacement of 60% of fishmeal with yeast mixture resulted in lower specific growth rate of 1.0% versus 1.2%/day for other diets. Apparent digestibility coefficients for crude protein and most amino acids were highest in fish fed fishmeal‐based diet, with similar values for fish fed the diet with 20% replacement with yeast mixture. Diet with 20% replacement with yeast mixture resulted in highest phosphorus digestibility. Replacement of 60% of fishmeal with S. cerevisiae resulted in oedematous mucosal fold tips in the proximal intestine. The results of this study suggest that these yeasts can replace up to 40% of fishmeal under current inclusion levels in diets for rainbow trout without compromising growth performance, nutrient digestibility or intestinal health.     

Landscape simplification promotes weed seed predation by carabid beetles (Coleoptera: Carabidae)

Weeds constitute major constraints for farmers by reducing crop yield and quality. However, weeds are managed effectively using herbicides, but this may cause harmful effects on human health and the environment. In an experiment on weed seed predation, we tested the biological control potential of carabid beetles to combat weeds in the absence of herbicides. Seeds from three common weed species were placed in cereal fields on conventional and organic farms located along a landscape complexity gradient (area annual crops within 1 km) in two distinct regions in Sweden. Carabid beetles were sampled in the same fields using pitfall traps. Neither carabid species richness nor seed removal was related to organic farming. Seed removal was significantly related to carabid species richness and both carabid species richness and seed removal was higher in landscapes with large total area of annual crops, although the evenness of the carabid communities was lower. The carabid genera with strongest positive relationship to seed removal differed between regions (Trechus in Uppland and Pterostichus in Scania), as did the preference for the different weed seed species. This study concludes that carabid species richness contributes to weed seed predation and that large scale landscape context explains more variation in the carabids’ responses than local farming practices.     

Pheromone signaling mechanisms in yeast: a prototypical sex machine

The actions of many extracellular stimuli are elicited by complexes of cell surface receptors, heterotrimeric guanine nucleotide-binding proteins (G proteins), and mitogen-activated protein (MAP) kinase complexes. Analysis of haploid yeast cells and their response to peptide mating pheromones has produced important advances in our understanding of G protein and MAP kinase signaling mechanisms. Many of the components, their interrelationships, and their regulators were first identified in yeast. Current analysis of the pheromone response pathway (see the Connections Maps at Science's Signal Transduction Knowledge Environment) will benefit from new and powerful genomic, proteomic, and computational approaches that will likely reveal additional general principles that are applicable to more complex organisms.