Efficient use and recycling of the micronutrient iodide in mammals

Daily ingestion of iodide alone is not adequate to sustain production of the thyroid hormones, tri- and tetraiodothyronine. Proper maintenance of iodide in vivo also requires its active transport into the thyroid and its salvage from mono- and diiodotyrosine that are formed in excess during hormone biosynthesis. The enzyme iodotyrosine deiodinase responsible for this salvage is unusual in its ability to catalyze a reductive dehalogenation reaction dependent on a flavin cofactor, FMN. Initial characterization of this enzyme was limited by its membrane association, difficult purification and poor stability. The deiodinase became amenable to detailed analysis only after identification and heterologous expression of its gene. Site-directed mutagenesis recently demonstrated that cysteine residues are not necessary for enzymatic activity in contrast to precedence set by other reductive dehalogenases. Truncation of the N-terminal membrane anchor of the deiodinase has provided a soluble and stable source of enzyme sufficient for crystallographic studies. The structure of an enzyme·substrate co-crystal has become invaluable for understanding the origins of substrate selectivity and the mutations causing thyroid disease in humans.     

A Temporally Explicit Production Efficiency Model for Fuel Load Allocation in Southern Africa

Abstract We present a regional fuel load model (1 km² spatial resolution) applied in the southern African savanna region. The model is based on a patch-scale production efficiency model (PEM) scaled up to the regional level using empirical relationships between patch-scale behavior and multi-source remote sensing data (spatio-temporal variability of vegetation and climatic variables). The model requires the spatial distribution of woody vegetation cover, which is used to determine separate respiration rates for tree and grass. Net primary production, grass and tree leaf death, and herbivory are also taken into account in this mechanistic modeling approach. The fuel load model has been calibrated and validated from independent measurements taken from savanna vegetation in Africa southward from the equator. A sensitivity analysis on the effect of climate variables (incoming radiation, air temperature, and precipitation) has been conducted to demonstrate the strong role that water availability has in determining productivity and subsequent fuel load over the southern African region. The model performance has been tested in four different areas representative of a regional increasing rainfall gradient—Etosha National Park, Namibia, Mongu and Kasama, Zambia, as well as in Kruger National Park, South Africa. Within each area, we analyze model output from three different magnitudes of canopy coverage (<5, 30, and 50%). We find that fuel load ranges predicted by the model are globally in agreement with field measurements for the same year. High rainfall sustains green herbaceous production late in the dry season and delays tree leaf litter production. Effect of water on production varies across the rainfall gradient with delayed start of green material production in more arid regions.     

Inactivation of Escherichia coli pyruvate formate-lyase by hypophosphite: evidence for a rate-limiting phosphorus-hydrogen bond cleavage

Recently, Knappe and co-workers [Knappe, J., Neugebauer, F. A., Blaschkowski, H. P., & Ganzler, M. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 1332] have shown that the catalytically active form of pyruvate formate-lyase from Escherichia coli is associated with a protein-bound organic free radical which is quenched upon enzyme inactivation by oxygen or hypophosphite. Our interest in the chemical mechanism of this unusual enzymatic reaction has led us to investigate several key aspects of the inactivation of the lyase by hypophosphite and its relationship to the normal enzymatic reaction. We report here that the inactivation of both the free and acetylated forms of the lyase is subject to a primary kinetic isotope effect using [2H2]hypophosphite. This suggests that phosphorus-hydrogen bond cleavage is at least partially rate limiting during inactivation. In addition, the inactivated enzyme can be fully reactivated. We have also determined a Vmax/Km isotope effect of 3.6 +/- 0.7 for pyruvate formation from [2H]formate and acetyl coenzyme A. Thus, carbon-hydrogen bond cleavage is partially rate limiting in the normal reverse reaction. On the basis of our findings, the previous work of Knappe and co-workers, the likelihood that hypophosphite is a formate analogue, the known susceptibility of both hypophosphite and formate to homolysis, and a chemical precedent for homolytic cleavage of pyruvate, we offer a preliminary mechanistic proposal for the lyase reaction.     

Iron and Porphyrin Trafficking in Heme Biogenesis

Iron is an essential element for diverse biological functions. In mammals, the majority of iron is enclosed within a single prosthetic group: heme. In metazoans, heme is synthesized via a highly conserved and coordinated pathway within the mitochondria. However, iron is acquired from the environment and subsequently assimilated into various cellular pathways, including heme synthesis. Both iron and heme are toxic but essential cofactors. How is iron transported from the extracellular milieu to the mitochondria? How are heme and heme intermediates coordinated with iron transport? Although recent studies have answered some questions, several pieces of this intriguing puzzle remain unsolved.     

Modelling biomass of mountainous grasslands by including a species composition map

High mountain grasslands offer multiple goods and services to society but are severely threatened by improper land use practices such as abandonment or rapid intensification. In order to reduce abandonment and strengthen the common extensive agricultural practice a sustainable land use management of high mountain grasslands is needed. A spatially detailed yield assessment helps to identify possible meadows or, on the contrary, areas with a low carrying capacity in a region, making it easier to manage these sites. Such assessments are rarely available for remote and inaccessible areas. Remotely sensed vegetation indices are able to provide valuable information on grassland properties. These indices tend, however, to saturate for high biomass. This affects their applicability to assessments of high-yield grasslands.The main aim of this study was to model a spatially explicit grassland yield map and to test whether saturation issues can be tackled by consideration of plant species composition in the modelling process. The high mountain grassland of the subalpine belt (1800 – 2500 m a.s.l.) in the Kazbegi region, Greater Caucasus, Georgia, was chosen as test site for its strong species composition and yield gradients.We first modelled the species composition of the grassland described as metrically scaled gradients in the form of ordination axes by random forest regression. We then derived vegetation indices from Rapid Eye imagery, and topographic variables from a digital elevation model, which we used together with the multispectral bands as predictive variables. For comparison, we performed two yield models, one excluding the species composition maps and one including the species composition map as predictors. Moreover, we performed a third individual model, with species composition as predictors and a split dataset, to produce the final yield map.Three main grassland types were found in the vegetation analysis: Hordeum violaceum-meadows, Gentianella caucasea-grassland and Astragalus captiosus-grassland. The three random forest regression models for the ordination axes explained 64%, 33% and 46% of the variance in species composition. Independent validation of modelled ordination scores against a validation data set resulted in an R² of 0.64, 0.32 and 0.46 for the first, second and third axes, respectively. The model based on species composition resulted in a R² = 0.55, whereas the benchmark model showed weaker relationships between yield and the multispectral reflectance, vegetation indices, and topographical parameters (R² = 0.42). The final random forest yield model used to derive the yield map resulted in 62% variance explained and an R² = 0.64 between predicted and observed biomass. The results further indicate that high yields are generally difficult to predict with both models.The benefit of including a species composition map as a predictor variable for grassland yield lies in the preservation of ecologically meaningful features, especially the occurrence of high yielding vegetation type of Hordeum violaceum meadows is depicted accurately in the map. Even though we used a gradient based design, sharp boundaries or immediate changes in productivity were visible, especially in small structures such as arable fields or roads (Fig. 6b), making it a valuable tool for sustainable land use management. The saturation effect however, was mitigated by using species composition as predictor variables but is still present at high yields.     

Determinants of expression variability

The amount of tissue-specific expression variability (EV) across individuals is an essential characteristic of a gene and believed to have evolved, in part, under functional constraints. However, the determinants and functional implications of EV are only beginning to be investigated. Our analyses based on multiple expression profiles in 41 primary human tissues show that a gene’s EV is significantly correlated with a number of features pertaining to the genomic, epigenomic, regulatory, polymorphic, functional, structural and network characteristics of the gene. We found that (i) EV of a gene is encoded, in part, by its genomic context and is further influenced by the epigenome; (ii) strong promoters induce less variable expression; (iii) less variable gene loci evolve under purifying selection against copy number polymorphisms; (iv) genes that encode inherently disordered or highly interacting proteins exhibit lower variability; and (v) genes with less variable expression are enriched for house-keeping functions, while genes with highly variable expression tend to function in development and extra-cellular response and are associated with human diseases. Thus, our analysis reveals a number of potential mediators as well as functional and evolutionary correlates of EV, and provides new insights into the inherent variability in eukaryotic gene expression.     

Genetic and physical characterization of proBA genes of the marine bacterium Vibrio parahaemolyticus

Intracellular proline pools have been implicated in the halotolerance of many organisms. To examine this relationship in a moderately halotolerant marine bacterium, Vibrio parahaemolyticus, proline biosynthesis genes were cloned in various plasmids. Some genetic and structural properties of those genes were examined. Subcloning showed that about 3.1 kilobases of V. parahaemolyticus DNA could complement proA and proB but not proC mutations of Escherichia coli. The same fragment would also complement some Pro- mutants of V. parahaemolyticus. Gamma-delta insertion mutagenesis of this subcloned fragment indicated that proB and proA genes of V. parahaemolyticus might be transcribed from different promoters. Two other genes, phoE and gpt, which map closely to the proBA genes in E. coli, were also found to be in close proximity to the proBA genes of V. parahaemolyticus.     

Macroinvertebrate drift in a Rocky Mountain stream

An extensive series of drift collections from a Rocky Mountain stream was used to investigate quantitative patterns in the taxonomic composition of drift throughout spring, summer and fall for 1975–1978. Drift was estimated by drift rate, the number of organisms drifting past a point per 24 h; and by drift density, the numbers of organisms collected per 100 m³ of water sampled.Drift densities were up to ten times greater by night than by day, and 24 h drift densities for the total fauna approached 2000 per 100 m³ in June–July, declining to <500 by autumn. Ephemeroptera, and especially Baetis, dominated the drift. Drift rates were greatest in late spring, around 10⁶ per 24 h, which are among the highest values reported for small trout streams. Drift rates declined to <10⁵ during the summer, and shifts in the taxonomic composition are described.Multiple regression analysis of the relationship between drift rate and density, and the independent variables discharge, benthic density and temperature, showed that discharge typically was a significant predictor of 24 h drift rate, usually the best single predictor. In contrast, 24 h drift density most frequently was independent of discharge, indicating that this measure tends to correct for seasonal variation in discharge, as suggested in the literature. However, this was not invariably true. Drift density significantly correlated with benthic density in five of eight taxa inspected, thus seasonal declines in the benthos probably accounted for parallel declines in drift density.