Transcriptome and membrane fatty acid analyses reveal different strategies for responding to permeating and non-permeating solutes in the bacterium Sphingomonas wittichii.

ABSTRACT: BACKGROUND: Sphingomonas wittichii strain RW1 can completely oxidize dibenzo-p-dioxins and dibenzofurans, which are persistent contaminants of soils and sediments. For successful application in soil bioremediation systems, strain RW1 must cope with fluctuations in water availability, or water potential. Thus far, however, little is known about the adaptive strategies used by Sphingomonas bacteria to respond to changes in water potential. To improve our understanding, strain RW1 was perturbed with either the cell-permeating solute sodium chloride or the non-permeating solute polyethylene glycol with a molecular weight of 8000 (PEG8000). These solutes are assumed to simulate the solute and matric components of the total water potential, respectively. The responses to these perturbations were then assessed and compared using a combination of growth assays, transcriptome profiling, and membrane fatty acid analyses. RESULTS: Under conditions producing a similar decrease in water potential but without effect on growth rate, there was only a limited shared response to perturbation with sodium chloride or PEG8000. This shared response included the increased expression of genes involved with trehalose and exopolysaccharide biosynthesis and the reduced expression of genes involved with flagella biosynthesis. Mostly, the responses to perturbation with sodium chloride or PEG8000 were very different. Only sodium chloride triggered the increased expression of two ECF-type RNA polymerase sigma factors and the differential expression of many genes involved with outer membrane and amino acid metabolism. In contrast, only PEG8000 triggered the increased expression of a heat shock-type RNA polymerase sigma factor along with many genes involved with protein turnover and repair. Membrane fatty acid analyses further corroborated these differences. The degree of saturation of membrane fatty acids increased after perturbation with sodium chloride but had the opposite effect and decreased after perturbation with PEG8000. CONCLUSIONS: A combination of growth assays, transcriptome profiling, and membrane fatty acid analyses revealed that permeating and non-permeating solutes trigger different adaptive responses in strain RW1, suggesting these solutes affect cells in fundamentally different ways. Future work is now needed that connects these responses with the responses observed in more realistic scenarios of soil desiccation.

First record of Anthomyiidae (Diptera) from New Caledonia with key to Australasian and Oceanian species of Anthomyia Meigen

The Anthomyiidae (Diptera) are known from about 1,100 species mostly occurring in temperate to arctic areas in the northern hemisphere. Few species have been reported from the Australasian and Oceanian Regions. New Caledonia, located in Melanesia, in the southwest Pacific Ocean, is well known for its high diversity, endemism and large number of unknown species. Specimens of Anthomyia Meigen from New Caledonia were found at the Muséum national d'Histoire naturelle (Paris) collection. The species was identified as A. medialis Colless, and represents the first record of Anthomyiidae from the island. A key to the Anthomyia species occurring in these regions is presented, as well as illustrations of the male terminalia of A. medialis.

Entomofauna associated to fruits and seeds of two species of Enterolobium Mart. (Leguminosae): harm or benefit?

Entomofauna associated to fruits and seeds of two species of Enterolobium Mart. (Leguminosae): Harm or benefit? The aims of the present study were to identify the entomofauna associated to the fruits and seeds of Enterolobium contortisiliquum (Vell.) Morong and Enterolobium timbouva Mart. (Leguminosae), as well as to determine relationships among insects and the possible harm and/or benefit stemming from these associations. Fruit infestation was evaluated and the insects were identified. Seed consumption (%) and the germination of predated seeds (%) were determined. The fruits of E. contortisiliquum exhibited a high percentage of infestation (91%). The most representative species in the fruits were Lophopoeum timbouvae Lameere, 1884, Merobruchus bicoloripes (Pic, 1930) and Stator limbatus (Horn, 1873). In the fruits of E. timbouva, only one species was found (S. limbatus). E. contortisiliquum seed consumption was proportionately higher (55.2%) to that of E. timbouva (15%). The germination of predated seeds from E. contortisiliquum was null, whereas 40% of predated seeds from E. timbouva germinated.

Testing the response of macroinvertebrate functional structure and biodiversity to flooding and confinement

The aim of the present study was to investigate the relative importance of flooding- and confinement-related environmentalfeatures in explaining macroinvertebrate trait structure and diversity in a pool of wetlands located in a Mediterranean riverfloodplain. To test hypothesized trait-environment relationships, we employed a recently implemented statistical procedure, thefourth-corner method. We found that flooding-related variables, mainly pH and turbidity, were related to traits that confer an abilityof the organism to resist flooding (e.g., small body-shape, protection of eggs) or recuperate faster after flooding (e.g., short life-span, asexual reproduction). In contrast, confinement-related variables, mainly temperature and organic matter, enhanced traits that allow organisms to interact and compete with other organisms (e.g., large size, sexual reproduction) and to efficiently use habitat and resources (e.g., diverse locomotion and feeding strategies). These results are in agreement with predictions made under the River Habitat Templet for lotic ecosystems, and demonstrate the ability of the fourth-corner method to test hypothesis that posit traitenvironment relationships. Trait diversity was slightly higher in flooded than in confined sites, whereas trait richness was not significantly different. This suggests that although trait structure may change in response to the main environmental factors, as evidenced by the fourth-corner method, the number of life-history strategies needed to persist in the face of such constraints remains more or less constant; only their relative dominance differs

HIERFSTAT, a package for R to compute and test hierarchical F-statistics

The package HIERFSTAT for the statistical software R, created by the R Development Core Team, allows the estimate of hierarchical F-statistics from a hierarchy with any numbers of levels. In addition, it allows testing the statistical significance of population differentiation for these different levels, using a generalized likelihood-ratio test. The package HIERFSTAT is available at http://www.unil.ch/popgen/softwares/hierfstat.htm.

Socio-economic benefits of using space technologies to monitor and respond to earthquakes

Earthquakes represent a major hazard for populations around the world, causing frequent loss of life,human suffering and enormous damage to homes, other buildings and infrastructure. The Technology Resources forEarthquake Monitoring and Response (TREMOR) Team of 36 space professionals analysed this problem over thecourse of the International Space University Summer Session Program and published their recommendations in the formof a report. The TREMOR Team proposes a series of space- and ground-based systems to provide improved capabilityto manage earthquakes. The first proposed system is a prototype earthquake early-warning system that improves theexisting knowledge of earthquake precursors and addresses the potential of these phenomena. Thus, the system willat first enable the definitive assessment of whether reliable earthquake early warning is possible through precursormonitoring. Should the answer be affirmative, the system itself would then form the basis of an operational earlywarningsystem. To achieve these goals, the authors propose a multi-variable approach in which the system will combine,integrate and process precursor data from space- and ground-based seismic monitoring systems (already existing andnew proposed systems) and data from a variety of related sources (e.g. historical databases, space weather data, faultmaps). The second proposed system, the prototype earthquake simulation and response system, coordinates the maincomponents of the response phase to reduce the time delays of response operations, increase the level of precisionin the data collected, facilitate communication amongst teams, enhance rescue and aid capabilities and so forth. It isbased in part on an earthquake simulator that will provide pre-event (if early warning is proven feasible) and post-eventdamage assessment and detailed data of the affected areas to corresponding disaster management actors by means of ageographic information system (GIS) interface. This is coupled with proposed mobile satellite communication hubs toprovide links between response teams. Business- and policy-based implementation strategies for these proposals, suchas the establishment of a non-governmental organisation to develop and operate the systems, are included.

An evolutionary model explaining the Neolithic transition from egalitarianism to leadership and despotism.

The Neolithic was marked by a transition from small and relatively egalitarian groups to much larger groups with increased stratification. But, the dynamics of this remain poorly understood. It is hard to see how despotism can arise without coercion, yet coercion could not easily have occurred in an egalitarian setting. Using a quantitative model of evolution in a patch-structured population, we demonstrate that the interaction between demographic and ecological factors can overcome this conundrum. We model the coevolution of individual preferences for hierarchy alongside the degree of despotism of leaders, and the dispersal preferences of followers. We show that voluntary leadership without coercion can evolve in small groups, when leaders help to solve coordination problems related to resource production. An example is coordinating construction of an irrigation system. Our model predicts that the transition to larger despotic groups will then occur when: (i) surplus resources lead to demographic expansion of groups, removing the viability of an acephalous niche in the same area and so locking individuals into hierarchy; (ii) high dispersal costs limit followers' ability to escape a despot. Empirical evidence suggests that these conditions were probably met, for the first time, during the subsistence intensification of the Neolithic.

Homeostatic and circadian contribution to EEG and molecular state variables of sleep regulation.

STUDY OBJECTIVES: Besides their well-established role in circadian rhythms, our findings that the forebrain expression of the clock-genes Per2 and Dbp increases and decreases, respectively, in relation to time spent awake suggest they also play a role in the homeostatic aspect of sleep regulation. Here, we determined whether time of day modulates the effects of elevated sleep pressure on clock-gene expression. Time of day effects were assessed also for recognized electrophysiological (EEG delta power) and molecular (Homer1a) markers of sleep homeostasis. DESIGN: EEG and qPCR data were obtained for baseline and recovery from 6-h sleep deprivation starting at ZT0, -6, -12, or -18. SETTING: Mouse sleep laboratory. PARTICIPANTS: Male mice. INTERVENTIONS: Sleep deprivation. RESULTS: The sleep-deprivation induced changes in Per2 and Dbp expression importantly varied with time of day, such that Per2 could even decrease during sleep deprivations occurring at the decreasing phase in baseline. Dbp showed similar, albeit opposite dynamics. These unexpected results could be reliably predicted assuming that these transcripts behave according to a driven damped harmonic oscillator. As expected, the sleep-wake distribution accounted for a large degree of the changes in EEG delta power and Homer1a. Nevertheless, the sleep deprivation-induced increase in delta power varied also with time of day with higher than expected levels when recovery sleep started at dark onset. CONCLUSIONS: Per2 and delta power are widely used as exclusive state variables of the circadian and homeostatic process, respectively. Our findings demonstrate a considerable cross-talk between these two processes. As Per2 in the brain responds to both sleep loss and time of day, this molecule is well positioned to keep track of and to anticipate homeostatic sleep need. CITATION: Curie T; Mongrain V; Dorsaz S; Mang GM; Emmenegger Y; Franken P. Homeostatic and circadian contribution to EEG and molecular state variables of sleep regulation. SLEEP 2013;36(3):311-323.

Modification de la composition des cigarettes durant te XXe siècle: rôle de l'industrie du tabac et effet sur la dépendance tabagique [Chemicals added to cigarettes and their effects on tobacco dependence]

This paper summarizes data on the factors involved in addiction and dependence to cigarettes. Nicotine has been intensively studied by the tobacco industry, for instance for its addictive effect at the lowest possible rates. The addition of diammonium phosphate and urea produces an alcalinization of the pH of cigarette smoke, and promotes the absorption and the trans-membrane passage of nicotine. The taste, the smell of smoke, and the visual aspect of the pack of cigarettes are also sensory components that promote addiction. Finally, menthol, sugar, cocoa and liquorice added to cigarettes also play a role in dependence and addiction to cigarettes by, for instance, making an anesthetic effect on the airways.

Reconsolidation of the soil surface after tillage discontinuity, with and without cultivation, related to erosion and its prediction with RUSLE

Site-specific regression coefficient values are essential for erosion prediction with empirical models. With the objective to investigate the surface-soilconsolidation factor, Cf, linked to the RUSLE's prior-land-use subfactor, PLU, an erosion experiment using simulated rainfall on a 0.075 m m-1 slope, sandy loam Paleudult soil, was conducted at the Agriculture Experimental Station of the Federal University of Rio Grande do Sul (EEA/UFRGS), in Eldorado do Sul, State of Rio Grande do Sul, Brazil. Firstly, a row-cropped area was excluded from cultivation (March 1995), the existing crop residue removed from the field, and the soil kept clean-tilled the rest of the year (to get a degraded soil condition for the intended purpose of this research). The soil was then conventional-tilled for the last time (except for a standard plot which was kept continuously cleantilled for comparison purposes), in January 1996, and the following treatments were established and evaluated for soil reconsolidation and soil erosion until May 1998, on duplicated 3.5 x 11.0 m erosion plots: (a) fresh-tilled soil, continuously in clean-tilled fallow (unit plot); (b) reconsolidating soil without cultivation; and (c) reconsolidating soil with cultivation (a crop sequence of three corn- and two black oats cycles, continuously in no-till, removing the crop residues after each harvest for rainfall application and redistributing them on the site after that). Simulated rainfall was applied with a Swanson's type, rotating-boom rainfall simulator, at 63.5 mm h-1 intensity and 90 min duration, six times during the two-and-half years of experimental period (at the beginning of the study and after each crop harvest, with the soil in the unit plot being retilled before each rainfall test). The soil-surface-consolidation factor, Cf, was calculated by dividing soil loss values from the reconsolidating soil treatments by the average value from the fresh-tilled soil treatment (unit plot). Non-linear regression was used to fit the Cf = e b.t model through the calculated Cf-data, where t is time in days since last tillage. Values for b were -0.0020 for the reconsolidating soil without cultivation and -0.0031 for the one with cultivation, yielding Cf-values equal to 0.16 and 0.06, respectively, after two-and-half years of tillage discontinuation, compared to 1.0 for fresh-tilled soil. These estimated Cf-values correspond, respectively, to soil loss reductions of 84 and 94 %, in relation to soil loss from the fresh-tilled soil, showing that the soil surface reconsolidated intenser with cultivation than without it. Two distinct treatmentinherent soil surface conditions probably influenced the rapid decay-rate of Cf values in this study, but, as a matter of a fact, they were part of the real environmental field conditions. Cf-factor curves presented in this paper are therefore useful for predicting erosion with RUSLE, but their application is restricted to situations where both soil type and particular soil surface condition are similar to the ones investigate in this study.

Surface and subsurface decomposition of a desiccated grass pasture biomass related to erosion and its prediction with RUSLE

Erosion is deleterious because it reduces the soil's productivity capacity for growing crops and causes sedimentation and water pollution problems. Surface and buried crop residue, as well as live and dead plant roots, play an important role in erosion control. An efficient way to assess the effectiveness of such materials in erosion reduction is by means of decomposition constants as used within the Revised Universal Soil Loss Equation - RUSLE's prior-land-use subfactor - PLU. This was investigated using simulated rainfall on a 0.12 m m-1 slope, sandy loam Paleudult soil, at the Agriculture Experimental Station of the Federal University of Rio Grande do Sul, in Eldorado do Sul, State of Rio Grande do Sul, Brazil. The study area had been covered by native grass pasture for about fifteen years. By the middle of March 1996, the sod was mechanically mowed and the crop residue removed from the field. Late in April 1996, the sod was chemically desiccated with herbicide and, about one month later, the following treatments were established and evaluated for sod biomass decomposition and soil erosion, from June 1996 to May 1998, on duplicated 3.5 x 11.0 m erosion plots: (a) and (b) soil without tillage, with surface residue and dead roots; (c) soil without tillage, with dead roots only; (d) soil tilled conventionally every two-and-half months, with dead roots plus incorporated residue; and (e) soil tilled conventionally every six months, with dead roots plus incorporated residue. Simulated rainfall was applied with a rotating-boom rainfall simulator, at an intensity of 63.5 mm h-1 for 90 min, eight to nine times during the experimental period (about every two-and-half months). Surface and subsurface sod biomass amounts were measured before each rainfall test along with the erosion measurements of runoff rate, sediment concentration in runoff, soil loss rate, and total soil loss. Non-linear regression analysis was performed using an exponential and a power model. Surface sod biomass decomposition was better depicted by the exponential model, while subsurface sod biomass was by the power model. Subsurface sod biomass decomposed faster and more than surface sod biomass, with dead roots in untilled soil without residue on the surface decomposing more than dead roots in untilled soil with surface residue. Tillage type and frequency did not appreciably influence subsurface sod biomass decomposition. Soil loss rates increased greatly with both surface sod biomass decomposition and decomposition of subsurface sod biomass in the conventionally tilled soil, but they were minimally affected by subsurface sod biomass decomposition in the untilled soil. Runoff rates were little affected by the studied treatments. Dead roots plus incorporated residues were effective in reducing erosion in the conventionally tilled soil, while consolidation of the soil surface was important in no-till. The residual effect of the turned soil on erosion diminished gradually with time and ceased after two years.