A new class of hexahelical insect proteins revealed as putative carriers of small hydrophobic ligands

BACKGROUND: THP12 is an abundant and extraordinarily hydrophilic hemolymph protein from the mealworm Tenebrio molitor and belongs to a group of small insect proteins with four highly conserved cysteine residues. Despite their sequence homology to odorant-binding proteins and pheromone-binding proteins, the function of these proteins is unclear. RESULTS: The first three-dimensional structure of THP12 has been determined by multidimensional NMR spectroscopy. The protein has a nonbundle helical structure consisting of six alpha helices. The arrangement of the alpha helices has a 'baseball glove' shape. In addition to the hydrophobic core, electrostatic interactions make contributions to the overall stability of the protein. NMR binding studies demonstrated the binding of small hydrophobic ligands to the single hydrophobic groove in THP12. Comparing the structure of THP12 with the predicted secondary structure of homologs reveals a common fold for this new class of insect proteins. A search with the program DALI revealed extensive similarity between the three-dimensional structure of THP12 and the N-terminal domain (residues 1-95) of recoverin, a member of the family of calcium-binding EF-hand proteins. CONCLUSIONS: Although the biological function of this new class of proteins is as yet undetermined, a general role as alpha-helical carrier proteins for small hydrophobic ligands, such as fatty acids or pheromones, is proposed on the basis of NMR-shift perturbation spectroscopy.     

Predation risk and abiotic habitat parameters affect personality traits in extremophile populations of a neotropical fish (Poecilia vivipara)

Understanding whether and how ambient ecological conditions affect the distribution of personality types within and among populations lies at the heart of research on animal personality. Several studies have focussed on only one agent of divergent selection (or driver of plastic changes in behavior), considering either predation risk or a single abiotic ecological factor. Here, we investigated how an array of abiotic and biotic environmental factors simultaneously shape population differences in boldness, activity in an open‐field test, and sociability/shoaling in the livebearing fish Poecilia vivipara from six ecologically different lagoons in southeastern Brazil. We evaluated the relative contributions of variation in predation risk, water transparency/visibility, salinity (ranging from oligo‐ to hypersaline), and dissolved oxygen. We also investigated the role played by environmental factors for the emergence, strength, and direction of behavioral correlations. Water transparency explained most of the behavioral variation, whereby fish from lagoons with low water transparency were significantly shyer, less active, and shoaled less than fish living under clear water conditions. When we tested additional wild‐caught fish from the same lagoons after acclimating them to homogeneous laboratory conditions, population differences were largely absent, pointing toward behavioral plasticity as a mechanism underlying the observed behavioral differences. Furthermore, we found correlations between personality traits (behavioral syndromes) to vary substantially in strength and direction among populations, with no obvious associations with ecological factors (including predation risk). Altogether, our results suggest that various habitat parameters simultaneously shape the distribution of personality types, with abiotic factors playing a vital (as yet underestimated) role. Furthermore, while predation is often thought to lead to the emergence of behavioral syndromes, our data do not support this assumption.     

Differentiation of movement behaviour in an adaptively diverging salamander population

Dispersal is considered to be a species‐specific trait, but intraspecific variation can be high. However, when and how this complex trait starts to differentiate during the divergence of species/lineages is unknown. Here, we studied the differentiation of movement behaviour in a large salamander population (Salamandra salamandra), in which individual adaptations to different habitat conditions drive the genetic divergence of this population into two subpopulations. In this system, salamanders have adapted to the deposition and development of their larvae in ephemeral ponds vs. small first‐order streams. In general, the pond habitat is characterized as a spatially and temporally highly unpredictable habitat, while streams provide more stable and predictable conditions for the development of larvae. We analysed the fine‐scale genetic distribution of larvae, and explored whether the adaptation to different larval habitat conditions has in turn also affected dispersal strategies and home range size of adult salamanders. Based on the genetic assignment of adult individuals to their respective larval habitat type, we show that pond‐adapted salamanders occupied larger home ranges, displayed long‐distance dispersal and had a higher variability of movement types than the stream‐adapted individuals. We argue that the differentiation of phenotypically plastic traits such as dispersal and movement characteristics can be a crucial component in the course of adaptation to new habitat conditions, thereby promoting the genetic divergence of populations.     

Patterns and regulation of silicon accumulation in Synechococcus spp.

Six clones of the marine cyanobacterium Synechococcus, representing four major clades, were all found to contain significant amounts of silicon in culture. Growth rate was unaffected by silicic acid, Si(OH)₄, concentration between 1 and 120 μM suggesting that Synechococcus lacks an obligate need for silicon (Si). Strains contained two major pools of Si: an aqueous soluble and an aqueous insoluble pool. Soluble pool sizes correspond to estimated intracellular dissolved Si concentrations of 2–24 mM, which would be thermodynamically unstable implying the binding of intracellular soluble Si to organic ligands. The Si content of all clones was inversely related to growth rate and increased with higher [Si(OH)₄] in the growth medium. Accumulation rates showed a unique bilinear response to increasing [Si(OH)₄] from 1 to 500 μM with the rate of Si acquisition increasing abruptly between 80 and 100 μM Si(OH)₄. Although these linear responses imply some form of diffusion‐mediated transport, Si uptake rates at low Si (~1 μM Si) were inhibited by orthophosphate, suggesting a role of phosphate transporters in Si acquisition. Theoretical calculations imply that observed Si acquisition rates are too rapid to be supported by lipid‐solubility diffusion of Si through the plasmalemma; however, facilitated diffusion involving membrane protein channels may suffice. The data are used to construct a working model of the mechanisms governing the Si content and rate of Si acquisition in Synechococcus.     

Extreme spring conditions in the Arctic delay spring phenology of long-distance migratory songbirds

Arctic regions are warming rapidly, with extreme weather events increasing in frequency, duration, and intensity just as in other regions. Many studies have focused on how shifting seasonality in environmental conditions affects vegetation phenology, while far fewer have examined how the breeding phenology of arctic fauna responds. We studied two species of long-distance migratory songbirds, Lapland longspurs, Calcarius lapponicus, and white-crowned sparrows, Zonotrichia leucophrys gambelii, across five consecutive breeding seasons in northern Alaskan tundra. We aimed to understand how spring environmental conditions affected breeding cycle phenology, including the timing of arrival on breeding grounds, territory establishment, and clutch initiation. Spring temperatures, precipitation, and snow-free dates differed significantly among years, with 2013 characterized by unusually late snow cover. In response, we found a significant delay in breeding-cycle phenology for both study species in 2013 relative to other study years: the first bird observed was delayed by 6–10 days, with mean arrival by 3–6 days, territory establishment by 6–13 days, and clutch initiation by 4–10 days. Further, snow cover, temperature, and precipitation during the territory establishment period were important predictors of clutch initiation dates for both species. These findings suggest that Arctic-breeding passerine communities may have the flexibility required to adjust breeding phenology in response to the increasingly extreme and unpredictable environmental conditions—although future generations may encounter conditions that exceed their current range of phenological flexibility.     

Fully automated single-use stirred-tank bioreactors for parallel microbial cultivations

Single-use stirred tank bioreactors on a 10-mL scale operated in a magnetic-inductive bioreaction block for 48 bioreactors were equipped with individual stirrer-speed tracing, as well as individual DO- and pH-monitoring and control. A Hall-effect sensor system was integrated into the bioreaction block to measure individually the changes in magnetic field density caused by the rotating permanent magnets. A restart of the magnetic inductive drive was initiated automatically each time a Hall-effect sensor indicates one non-rotating gas-inducing stirrer. Individual DO and pH were monitored online by measuring the fluorescence decay time of two chemical sensors immobilized at the bottom of each single-use bioreactor. Parallel DO measurements were shown to be very reliable and independently from the fermentation media applied in this study for the cultivation of Escherichia coli and Saccharomyces cerevisiae. The standard deviation of parallel pH measurements was pH 0.1 at pH 7.0 at the minimum and increased to a standard deviation of pH 0.2 at pH 6.0 or at pH 8.5 with the complex medium applied for fermentations with S. cerevisiae. Parallel pH-control was thus shown to be meaningful with a tolerance band around the pH set-point of ± pH 0.2 if the set-point is pH 6.0 or lower.     

Protective effect of hop beta-acids on microbial degradation of thick juice during storage

Aims:  This study assessed the value of a commercial alkaline solution of hop β-acids (HBA) for prevention of microbial degradation of thick juice, a concentrated intermediate product in the production of beet sugar.
Methods and Results:  The antimicrobial effect of different concentrations of HBA against microbial degradation of thick juice was tested in a pilot-scale storage experiment. Chemical, biochemical and microbial parameters were monitored during thick juice storage. Thick juice degradation, indicated as a decrease in pH, was generally accompanied by an increase in the count of fastidious bacteria (FB) on Columbia Agar with Sheep Blood (CAwSB), which were mainly identified as Tetragenococcus halophilus . Addition of HBA delayed juice acidification and the development of FB in a concentration-dependent manner. The susceptibility of FB to HBA was determined by plating degraded thick juice (FB > 10⁵ CFU ml⁻¹) on CAwSB plates with different concentrations of HBA (0–160 ppm). None of the HBA concentrations tested reduced the number of FB colonies formed, but increasing HBA concentrations extended the lag time of colony formation.
Conclusions:  HBA produce no measurable bactericidal effect, but retard the development of FB in thick juice. Moreover, HBA do not prevent the thick juice from deteriorating, but significantly delay its degradation.
Significance and Impact of the Study:  These results indicate that adding a commercially available HBA formulation can prolong the storage life of thick juice in the sugar industry, although degradation cannot be eliminated. Future research will focus on the detailed characterization of FB consistently isolated from degraded thick juice and on determining their role in thick juice degradation.     

RReportGenerator: automatic reports from routine statistical analysis using R

With the establishment of high-throughput (HT) screening methods there is an increasing need for automatic analysis methods. Here we present RReportGenerator, a user-friendly portal for automatic routine analysis using the statistical platform R and Bioconductor. RReportGenerator is designed to analyze data using predefined analysis scenarios via a graphical user interface (GUI). A report in pdf format combining text, figures and tables is automatically generated and results may be exported. To demonstrate suitable analysis tasks we provide direct web access to a collection of analysis scenarios for summarizing data from transfected cell arrays (TCA), segmentation of CGH data, and microarray quality control and normalization. AVAILABILITY: RReportGenerator, a user manual and a collection of analysis scenarios are available under a GNU public license on http://www-bio3d-igbmc.u-strasbg.fr/~wraff     

Meeting the quest for spatial efficiency: progress and prospects of extensive aquaculture within offshore wind farms

Along the German North Sea coast, the observed high spatial competition of stakeholders has encouraged the idea of integrating open ocean aquaculture in conjunction with offshore wind farms beyond the 12 miles zone. The article provides an overview on the current state of transdisciplinary research on a potential implementation of such a multifunctional use concept on a showcase basis, covering biological, technical, economic and social/policy aspects as well as private–public partnerships and the relevant institutional bodies. We show that the cultivation of seaweeds and blue mussels is biologically and technically feasible in a high-energy environment using modified cultivation strategies. The point of departure of our multi-use concept was that the solid groundings of wind turbines could serve as attachment points for the aquaculture installations and become the key to the successful commercial cultivation of any offshore aquatic organism. However, spaces in between the turbines are also attractive for farming projects, since public access is restricted and thus the cultivation site protected from outside influences. An economic analysis of different operation scenarios indicates that the market price and the annual settlement success of juvenile mussels are the main factors that determine the breakeven point. Social and policy science research reveals that the integration of relevant actors into the development of a multi-use concept for a wind farm-mariculture interaction is a complex and controversial issue. Combining knowledge and experience of wind farm planners as well as mussel fishermen and mariculturists within the framework of national and EU policies is probably the most important component for designing and developing an effective offshore co-management regime to limit the consumption of ocean space.