Codon usage in the vertebrate hemoglobins and its implications

A study of codon usage in vertebrate hemoglobins revealed an evolutionary trend toward elevated numbers of CpG codon boundary pairs in mammalian hemoglobin alpha genes. Selection for CpG codon boundaries countering the generally observed CpG suppression is strongly suggested by these data. These observations parallel recently published experimental results that indicate that constitutive expression of the human alpha-globin gene appears to be determined by regulatory information encoded within the structural gene. The possibility is raised that, in the absence of selection, CpG decay can be used to date the evolutionary origin of a mammalian alpha pseudogene from its active alpha gene.      

Spectral quality of monochromatic LED affects photosynthetic acclimation to high-intensity sunlight of Chrysanthemum and Spathiphyllum

Vertical farming using light-emitting diode offers potential for the early production phase (few weeks) of young ornamental plants. However, once transferred to the greenhouse, the photosynthetic acclimation of these young plants might depend on this initial light regime. To obtain insight about this acclimatization, Chrysanthemum (sun species) and Spathiphyllum (shade species) were preconditioned in growth chambers for 4 weeks under four light qualities: blue (B), red (R), red/blue (RB, 60% R) and white (W) at 100 μmol m⁻² s⁻¹. Monochromatic light (R and B) limited leaf development of both species, which resulted in a lower leaf mass per area when compared to multispectral light (RB for Chrysanthemum, RB and W for Spathiphyllum). R-developed leaves had a lower photosynthetic efficiency in both species. After the light quality pretreatment, plants were transferred to the greenhouse with high-intensity natural light conditions. On the first day of transfer, R and B preconditioned leaves of both species had an inhibited photosynthesis. After 1 week in natural light condition, rapid light curve parameters of Chrysanthemum leaves that developed under B acclimated to sunlight had a similar level than RB-developed leaves unlike R-leaves. Spathiphyllum leaves showed a decrease in maximum electron transport rate and this was most pronounced for the R pretreatment. After 1 month, R-preconditioned Chrysanthemum had the lowest dry mass, while no effects on the dry weight of Spathiphyllum with respect to the pretreatments were observed. Light quality during preconditioning affected the leaf ability to acclimate to natural high light intensities in greenhouse environment.     

Automatic drought stress detection in grapevines without using conventional threshold values

Aims

Because the water status of grapevines strongly affects the quality of the grapes and resulting wine, automated and early drought stress detection is important. Plant measurements are very promising for detecting drought stress, but strongly depend on microclimatic changes. Therefore, conventional stress detection methods require threshold values which define when plants start sensing drought stress. There is however no unique method to define these values. In this study, we propose two techniques that overcome this limitation.

Methods

Two statistical methods were used to automatically distinguish between drought and microclimate effects, based on a short preceding full-irrigated period to extract plant behaviour under normal conditions: Unfold Principal Component Analysis (UPCA) and Functional Unfold Principal Component Analysis (FUPCA). Both techniques aimed at detecting when measured sap flow rate or stem diameter variations in grapevine deviated from their normal behaviour due to drought stress.

Results

The models based on sap flow rate had some difficulties to detect stress on days with low atmospheric demands, while those based on stem diameter variations did not show this limitation, but ceased detecting stress when the stem diameter levelled off after a period of severe shrinkage. Nevertheless, stress was successfully detected with both approaches days before visible symptoms appeared.

Conclusions

UPCA and FUPCA based on plant indicators are therefore very promising for early stress detection.     

Cyanobacterial-bacterial mat consortia: examining the functional unit of microbial survival and growth in extreme environments

Cyanobacterial–bacterial consortial associations are taxonomically complex, metabolically interactive, self-sustaining prokaryotic communities representing pioneer and often the only biota inhabiting extreme aquatic and terrestrial environments. Laminated mats and aggregates exemplify such communities. The fossil record indicates that these associations represent the earliest extant inhabitants and modifiers (i.e. anoxic to oxic conditions) of the Earth's biosphere. Present-day consortia flourish in physically and chemically stressed environments, including nutrient-deplete, hypersaline, calcified, desiccated and high-irradiance ecosystems ranging from the tropics to polar regions. Consortial members exhibit extensive metabolic diversification, but have remained structurally simple. Structural simplicity, while advantageous in countering environmental extremes, presents a 'packaging problem' with regard to compartmentalizing potentially cross-inhibitory aerobic versus anaerobic growth processes. To circumvent these metabolic constraints, phototrophic cyanobacteria and microheterotrophs orient along microscale chemical (i.e. O₂, pH, E _h) gradients to meet and optimize the biogeochemical processes (C, N, S cycling) essential for survival, growth and the maintenance of genetic diversity, needed to sustain life. Microscale ecophysiological, analytical, molecular (immunological and nucleic acid) techniques have helped to develop a mechanistic basis for understanding consortial growth and survival under extreme environmental conditions on Earth. Consortia are ideal model systems for developing a process-based understanding of the structural and functional requirements for life in extreme environments representative of the Earth's earliest biosphere and possibly other planets.     

Nitrogenase Activity and nifH Expression in a Marine Intertidal Microbial Mat

N₂ fixation, diazotrophic community composition, and organisms actively expressing genes for N₂ fixation were examined over at 3−year period (1997–1999) for intertidal microbial mats on a sand flat located in the Rachel Carson National Estuarine Research Reserve (RCNERR) (Beaufort, NC, USA). Specifically, diel variations of N₂ fixation in the mats from the RCNERR were examined. Three distinct diel patterns of nitrogenase activity (NA) were observed. NA responses to short-term inhibitions of photosynthesis corresponded to one of the three patterns. High rates of NA were observed during peak O₂ production periods for diel experiments during summer months. Different types of NA diel variations correspond to different stages of mat development. Chloramphenicol treatments indicated that the mechanism of protein synthesis supporting NA changed throughout the day. Analysis of mat DNA and RNA gave further evidence suggesting that in addition to cyanobacteria, other functional groups were responsible for the NA observed in the RCNERR mats. The role of microbial diversity in the N₂ fixation dynamics of these mats is discussed.     

Genetic Variance in the Composition of Two Functional Groups (Diazotrophs and Cyanobacteria) from a Hypersaline Microbial Mat

Examination of variation in ecological communities can lead to an understanding of the forces that structure communities, the consequences of change at the ecosystem level, and the relevant scales involved. This study details spatial and seasonal variability in the composition of nitrogen-fixing and cyanobacterial (i.e., oxygenic photosynthetic) functional groups of a benthic, hypersaline microbial mat from Salt Pond, San Salvador Island, Bahamas. This system shows extreme annual variability in the salinity of the overlying water and the extent of water coverage. Analysis of molecular variance and F_ST tests of genetic differentiation of nifH and cyanobacterial 16S rRNA gene clone libraries allowed for changes at multiple taxonomic levels (i.e., above, below, and at the species level) to inform the conclusions regarding these functional groups. Composition of the nitrogen-fixing community showed significant seasonal changes related to salinity, while cyanobacterial composition showed no consistent seasonal pattern. Both functional groups exhibited significant spatial variation, changing with depth in the mat and horizontally with distance from the shoreline. The patterns of change suggest that cyanobacterial composition was more insensitive to water stress, and consequently, cyanobacteria dominated the nitrogen-fixing community during dry months but gave way to a more diverse community of diazotrophs in wet months. This seasonal pattern may allow the mat community to respond quickly to water-freshening events after prolonged dry conditions (system recovery) and maintain ecosystem function in the face of disturbance during the wet season (system resilience).     

Identifiability analysis and improvement of a tree water flow and storage model

A recently published tree water flow and storage model (RCGro) for simulating water transport dynamics in trees and related stem diameter variations was improved in order to better describe a data set gathered under mild drought stress conditions. Model improvements were carried out based on the results of a mathematical identifiability analysis. This analysis provided important information with respect to the balance between model complexity and data availability. Using the identifiability analysis results, we were able to (1) highlight weaknesses of the model; (2) obtain information on how the model could be reduced in some places, to improve its identifiability properties, and extended in others, to enhance model performance; (3) identify which measurements are necessary to optimally calibrate the model. The resulting improved model was less complex (contained less unidentifiable parameters), had better dynamic properties and was able to better describe the stress data set.     

Stem respiration and carbon dioxide efflux of young <Emphasis Type="Italic">Populus deltoides</Emphasis> trees in relation to temperature and xylem carbon dioxide concentration

Oxidative respiration is strongly temperature driven. However, in woody stems, efflux of CO₂ to the atmosphere (E _A), commonly used to estimate the rate of respiration (R _S), and stem temperature (T _st) have often been poorly correlated, which we hypothesized was due to transport of respired CO₂ in xylem sap, especially under high rates of sap flow (f _s). To test this, we measured E _A, T _st, f _s and xylem sap CO₂ concentrations ([CO₂*]) in 3-year-old Populus deltoides trees under different weather conditions (sunny and rainy days) in autumn. We also calculated R _S by mass balance as the sum of both outward and internal CO₂ fluxes and hypothesized that R _S would correlate better with T _st than E _A. We found that E _A sometimes correlated well with T _st, but not on sunny mornings and afternoons or on rainy days. When the temperature effect on E _A was accounted for, a clear positive relationship between E _A and xylem [CO₂*] was found. [CO₂*] varied diurnally and increased substantially at night and during periods of rain. Changes in [CO₂*] were related to changes in f _s but not T _st. We conclude that changes in both respiration and internal CO₂ transport altered E _A. The dominant component flux of R _S was E _A. However, on a 24-h basis, the internal transport flux represented 9–18% and 3–7% of R _S on sunny and rainy days, respectively, indicating that the contribution of stem respiration to forest C balance may be larger than previously estimated based on E _A measurements. Unexpectedly, the relationship between R _S and T _st was sometimes weak in two of the three trees. We conclude that in addition to temperature, other factors such as water deficits or substrate availability exert control on the rate of stem respiration so that simple temperature functions are not sufficient to predict stem respiration.