Bottom-up synthetic biology: engineering in a tinkerer's world

How synthetic can "synthetic biology" be? A literal interpretation of the name of this new life science discipline invokes expectations of the systematic construction of biological systems with cells being built module by module--from the bottom up. But can this possibly be achieved, taking into account the enormous complexity and redundancy of living systems, which distinguish them quite remarkably from design features that characterize human inventions? There are several recent developments in biology, in tight conjunction with quantitative disciplines, that may bring this literal perspective into the realm of the possible. However, such bottom-up engineering requires tools that were originally designed by nature's greatest tinkerer: evolution.     

Spatial regulators for bacterial cell division self-organize into surface waves in vitro

In the bacterium Escherichia coli, the Min proteins oscillate between the cell poles to select the cell center as division site. This dynamic pattern has been proposed to arise by self-organization of these proteins, and several models have suggested a reaction-diffusion type mechanism. Here, we found that the Min proteins spontaneously formed planar surface waves on a flat membrane in vitro. The formation and maintenance of these patterns, which extended for hundreds of micrometers, required adenosine 5'-triphosphate (ATP), and they persisted for hours. We present a reaction-diffusion model of the MinD and MinE dynamics that accounts for our experimental observations and also captures the in vivo oscillations.     

Aesthetic preferences of non-farmers and farmers for different land-use types and proportions of ecological compensation areas in the Swiss lowlands

Beyond its traditional function of food production, agricultural land offers public amenities such as the protection of natural resources and landscape scenery. This study investigates the preferences of non-farmers and farmers for nine landscape scenarios in the Swiss lowlands. The nine landscapes were the result of a photo editing process combining three land-use types (arable crops, grassland and a mixture of both) and three proportions of ecological compensation areas (0%, 10% and 30%). The landscape photographs were randomly arranged on one page of a paper-based questionnaire which was sent to a random sample of 4000 Swiss households (non-farmers) and 500 farmers. The respondents (1376 non-farmers and 276 farmers) rated each landscape by attractiveness. Both non-farmers and farmers preferred a mixed land-use type or one dominated by arable crops over one dominated by grassland. Non-farmers’ preference ratings were highly influenced by the proportion of ecological compensation areas (ECAs) in the rated landscape: Non-farmers rated a landscape with a mixed land-use type and 30% ECAs highest, whereas farmers rated a landscape dominated by arable crops and 10% ECAs highest. The results indicate that heterogeneous landscapes (mixed land use, high proportion of ECAs) influence scenic beauty positively. Thus, farming practices and agro-environment schemes such as ECAs can have an impact on the visual attractiveness of a landscape.     

Effect of heat treatment of camelina (Camelina sativa) seeds on the antioxidant potential of their extracts

The effect of different heat treatments of camelina (Camelina sativa) seeds on the phenolic profile and antioxidant activity of their hydrolyzed extracts was investigated. The results showed that total phenol contents increased in thermally treated seeds. Heat treatment affected also the quantities of individual phenolic compounds in extracts. Phenolics in unheated camelina seeds existed in bound rather than in free form. A temperature of 160 °C was required for release of insoluble bound phenolics, whereas lower temperatures were found to be optimal to liberate those present as soluble conjugates. The best reducing power and alkyl peroxyl radical scavenging activity in the emulsion was expressed by phenolics which were bound to the cell wall, whereas the best iron chelators and 2,2-diphenyl-1-picrylhydrazyl (DPPH?) radical scavengers were found to be those present in free form. The heat treatment of seeds up to 120 °C increased the reducing power and DPPH? radical scavenging ability of extracts, but negatively affected iron chelating ability and their activity in an emulsion against alkyl peroxyl radicals.     

Relationships between carbon dioxide emission and soil properties in salt-affected landscapes

Net carbon dioxide (CO₂) emission from soils is controlled by the input rate of organic material and the rate of decomposition which in turn are affected by temperature, moisture and soil factors. While the relationships between CO₂ emission and soil factors are well-studied in non-salt-affected soils, little is known about soil properties controlling CO₂ emission from salt-affected soils. To close this knowledge gap, non-salt-affected and salt-affected soils (0-0.30 m) were collected from two agricultural regions: in India (irrigation induced salinity) and in Australia (salinity associated with ground water or non-ground water associated salinity). A subset (50 Indian and 70 Australian soils) covering the range of electrical conductivity (EC) and sodium adsorption ratio (SAR) in each region was used in a laboratory incubation experiment. The soils were left unamended or amended with mature wheat residues (2% w/w) and CO₂ release was measured over 120 days at constant temperature and soil water content. Residues were added to overcome carbon limitation for soil respiration. For the unamended soils, separation in multidimensional scaling plots was a function of differences in soil texture (clay, sand), SOC pools (particulate organic carbon (POC) and humus-C) and also EC. Cumulative CO₂-C emission from unamended and amended soils was related to soil properties by stepwise regression models. Cumulative CO₂-C emission was negatively correlated with EC in saline soils (R² = 0.50, p < 0.05) from both regions. In the unamended non-salt-affected soils, cumulative CO₂-C emission was significantly positively related to the content of POC for the Indian soils and negatively related to clay content for the Australian soils. In the wheat residue amended soils, cumulative CO₂-C emission had positive relationship with POC and humus-C but a negative correlation with EC for both Indian and Australian soils. SAR was negatively related (β = −0.66, p < 0.05) with cumulative CO₂-C emission only for the unamended saline-sodic soils of Australia. Cumulative CO₂-C emission was significantly negatively correlated with bulk density in amended soils from both regions. The study showed that in salt-affected soils, EC was the main factor influencing for soil respiration but the content of POC, humus-C and clay were also influential with the magnitude of influence depending on whether the soils were salt affected or not.     

Macrophakia in three cats

This report describes three cases of bilateral macrophakia in 3-, 5-, and 9-year-old cats, respectively. All cats were presented because of visual deficits. Ophthalmic examination revealed macrophakia (the vitreous was replaced by the lens) and retinal changes (tapetal hyper-reflectivity, attenuation of retinal vessels, and retinal folds) in all cats. In addition, bilateral subconjunctival orbital fat prolapse in one cat and microphthalmos in another cat were present. To confirm the ophthalmologic diagnosis of macrophakia, gross pathology examination in one cat and ultrasound examination in another cat were performed.     

Respiratory function and pulmonary lesions in pigs infected with porcine reproductive and respiratory syndrome virus

Pulmonary dysfunction was evaluated in pigs infected with porcine reproductive and respiratory syndrome virus (PRRSV, isolate VR-2332) and compared to clinical and pathological findings. Infected pigs developed fever, reduced appetite, respiratory distress and dullness at 9 days post-inoculation (dpi). Non-invasive pulmonary function tests using impulse oscillometry and rebreathing of test gases (He, CO) revealed peripheral airway obstruction, reduced lung compliance and reduced lung CO-transfer factor. PRRSV-induced pulmonary dysfunction was most marked at 9–18 dpi and was accompanied by a significantly increased respiratory rate and decreased tidal volume. Expiration was affected more than inspiration. On histopathological examination, multifocal areas of interstitial pneumonia (more severe and extensive at 10 dpi than 21 dpi) were identified as a possible structural basis for reduced lung compliance and gas exchange disturbances.     

Effect of drying and rewetting on phosphorus transformations in red brown soils with different soil organic matter content

In this study, the effect of drying and rewetting on native P transformations in two red brown soils with different management history was investigated. Three treatments, T1 (constantly moist), T2 (dried for 4 days and then kept dry), T3 (rewetted after 4 days drying) were used. Drying and rewetting caused a rapid increase in microbial P (Pm) and labile organic P (labile Po) within 1 day and a gradual increase in available inorganic P (Colwell). These increases were only temporarily, as Pm and labile Po decreased with time and were at the same level as in the constantly moist soil by the end of the incubation period of 21 days. The effect of drying and rewetting on P transformations strongly depended on soil organic matter content, being more pronounced in the soil with high organic matter content, compared to the soil with low soil organic matter content.     

Clay amendment to sandy soil—effect of clay concentration and ped size on nutrient dynamics after residue addition

Purpose

Crop growth on sandy soils can be increased by claying. In modified sandy soils, the added clay is in the form of peds ranging in size from millimetres to centimetres creating a highly non-uniform matrix where ped size could influence nutrient availability and organic C binding. The aim of the study was to determine the effect of clay addition rate and ped size in residue amended sandy soil on soil respiration, nutrient availability and organic C retention.

Materials and methods

In this study, clay peds of 1, 2 or 3 mm size derived from a clay-rich Vertosol (73 % clay) were added to a sandy soil (3 % clay) at clay addition rates of 10 and 20 % w/w. After the addition of ground faba bean residue (C/N 37) at 10 g kg^?1, the soils were incubated for 45 days at 80 % of water-holding capacity.

Results and discussion

Clay addition had no consistent effect on cumulative respiration, but reduced NH₄ ⁺ availability with a greater reduction at 20 % compared to 10 % clay and with 1 and 2 mm compared to 3 mm peds. Sandy soil with clay peds had a greater maximum NH₄ ⁺ and P sorption capacity than sandy soil alone, and sorption capacity was higher at 20 % compared to 10 % clay addition and greater with 1 mm compared to 3 mm peds. Retrieval of clay peds at the end of the experiment showed ped breakdown during the experiment but also the formation of larger peds. Compared to the <53 μm fraction added at the start of the experiment, the total organic carbon (TOC) content of the <53 μm fraction was increased up to nearly two fold, particularly in the smaller peds (1 and 2 mm).

Conclusions

When sandy soils are amended with clay, N availability and organic C binding depend on both clay addition rate and ped size.

     

Relative effects of management and environmental conditions on performance and survival of populations of a terrestrial orchid, Dactylorhiza majalis

For population viability analysis of endangered orchid populations, it is crucial to disentangle the effects of weather and management from intrinsic orchid dynamics. When doing this, typically several months’ average temperatures and/or sums of precipitations are compared with some characteristics of plant performance. Here we tested, whether short averaging intervals (1-2 weeks) are more closely correlated with orchid performance. We used 5 years of data from five Dactylorhiza majalis populations, and have shown that the improvement of prediction by shortening the interval over which the temperatures are averaged or precipitation summed, even if detectable, is only weak and not significant. This, however, may be due to low weather variability during the study. Regarding the second aspect, the effect of management (presence or absence of mowing), we have found that leaf area of D. majalis at the regularly mown site was larger than that at the sites which were mown only once in 2 years, but we did not detect a significant effect of the absence of mowing on the incidence of flowering. Mowing can affect orchid performance in two ways: by reduced shading of orchids and by reducing competition with other species. Therefore, we have determined the co-occurring species associated with presence or absence of mowing and found that shading significantly affected the length of the flower stalk, the ratio of leaf width to leaf length at the end of the season, but did not affect seed weight and probability of flowering the next year. We conclude that the most appropriate management for D. majalis is mowing at least once a year, ideally at the end of June/beginning of July, after its fruiting.