A content-centric organization of the genetic code

The codon table for the canonical genetic code can be rearranged in such a way that the code is divided into four quarters and two halves according to the variability of their GC and purine contents, respectively. For prokaryotic genomes, when the genomic GC content increases, their amino acid contents tend to be restricted to the GC-rich quarter and the purine-content insensitive half, where all codons are fourfold degenerate and relatively mutation-tolerant. Conversely, when the genomic GC content decreases, most of the codons retract to the AUrich quarter and the purine-content sensitive half; most of the codons not only remain encoding physicochemically diversified amino acids but also vary when transversion （between purine and pyrimidine） happens. Amino acids with sixfolddegenerate codons are distributed into all four quarters and across the two halves; their fourfold-degenerate codons are all partitioned into the purine-insensitive half in favorite of robustness against mutations. The features manifested in the rearranged codon table explain most of the intrinsic relationship between protein coding sequences （the informational content） and amino acid compositions （the functional content）. The renovated codon table is useful in predicting abundant amino acids and positioning the amino acids with related or distinct physicochemical properties.     

Physicochemical characterization of ultrasmall superparamagnetic iron oxide particles (USPIO) for biomedical application as MRI contrast agents

Ultrasmall superparamagnetic iron oxide (USPIO) particles are maghemite or magnetite nanoparticles currently used as contrast agent in magnetic resonance imaging. The coatings surrounding the USPIO inorganic core play a major role in both the in vitro stability and, over all, USPIO's in vivo fate. Different physicochemical properties such as final size, surface charge and coating density are key factors in this respect. Up to now no precise structure--activity relationship has been described to predict entirely the USPIOs stability, as well as their pharmacokinetics and their safety. This review is focused on both the classical and the latest available techniques allowing a better insight in the magnetic core structure and the organic surface of these particles. Concurrently, this work clearly shows the difficulty to obtain a complete physicochemical characterization of USPIOs particles owing to their small dimensions, reaching the analytical resolution limits of many commercial instruments. An extended characterization is therefore necessary to improve the understanding of the properties of USPIOs when dispersed in an aqueous environment and to set the specifications and limits for their conception.     

Biological hydrogen production in a UASB reactor with granules. I: Physicochemical characteristics of hydrogen-producing granules

Hydrogen-producing granules with an excellent settling ability were cultivated in an upflow anaerobic sludge blanket reactor treating a sucrose-rich synthetic wastewater. The physicochemical characteristics of granules were evaluated in this study. The mature granules had a diameter ranging from 1.0 to 3.5 mm and an average density of 1.036 +/- 0.005 g/mL, whereas they had good settling ability and a high settling velocity of 32-75 m/h. The low ratio of proteins/carbohydrates for the extracellular polymeric substances (EPS) in the granules suggests that carbohydrates rather than proteins, might play a more important role in the formation of the H(2)-producing granules. The contact angle of the mature granules, 54 +/- 2 degrees , was larger than that of the seed sludge (38 +/- 2 degrees ), indicating that the microbial cells in the H(2)-producing granules had higher hydrophobicity. The granules had fractal nature with a fractal dimension of 1.78. Their porosities were in the range of 0-0.70, and increased with increasing granule size. The ratios between the observed and predicted settling velocities by Stokes' law were in a range of 1.00-1.50, and the fluid collection efficiency of the granules ranged from 0 to 0.19, indicating that their permeabilities were lower and that there was little advective flow through their interior. Experimental results also suggest that molecular diffusion appeared to play an important role in the mass transfer through the H(2)-producing granules.     

Characterization of the abiotic drivers of abundance of nearshore Arctic fishes

Fish are critical ecologically and socioeconomically for subsistence economies in the Arctic, an ecosystem undergoing unprecedented environmental change. Our understanding of the responses of nearshore Arctic fishes to environmental change is inadequate because of limited research on the physicochemical drivers of abundance occurring at a fine scale. Here, high‐frequency in situ measurements of pH, temperature, salinity, and dissolved oxygen were paired with daily fish catches in nearshore Alaskan waters of the Beaufort Sea. Due to the threat that climate change poses to high‐latitude marine ecosystems, our main objective was to characterize the abiotic drivers of abundance and elucidate how nearshore fish communities may change in the future. We used generalized additive models (GAMs) to describe responses to the nearshore environment for 18 fish species. Relationships between abundance and the physicochemical environment were variable between species and reflected life history. Each abiotic covariate was significant in at least one GAM, exhibiting both nonlinear and linear associations with abundance. Temperature was the most important predictor of abundance and was significant in GAMs for 11 species. Notably, pH was a significant predictor of abundance for six species: Arctic cod (Boreogadus saida), broad whitefish (Coregonus nasus), Dolly Varden (Salvelinus malma), ninespine stickleback (Pungitius pungitius), saffron cod (Eleginus gracilis), and whitespotted greenling (Hexagrammos stelleri). Broad whitefish and whitespotted greenling abundance was positively associated with pH, while Arctic cod and saffron cod abundance was negatively associated with pH. These results may be a bellwether for future nearshore Arctic fish community change by providing a foundational characterization of the relationships between abundance and the abiotic environment, particularly in regard to pH, and demonstrate the importance of including a wider range of physicochemical habitat covariates in future research.     

The Microhabitat Distribution of the Arkansas River Shiner, Notropis girardi: A Habitat-mosaic Approach

I evaluated the microhabitat distribution of the Arkansas River shiner, Notropis girardi, a candidate species for protection under the Endangered Species Act over a two-year period. Seasonal microhabitat samples were taken at three localities along the South Canadian River in central Oklahoma. The microhabitats sampled were defined subjectively based on structural and substrate characteristics: adjacent to stream banks, underwater sand ridges, or exposed sand islands, and within stream pools, midchannels, or backwaters. At each microhabitat, the following physicochemical measurements were made: depth, temperature, current speed, dissolved oxygen, conductivity, and pH. Notropis girardi used many microhabitats and the patterns varied seasonally and ontogenetically. Contingency tests indicated that bank, island, and sandridge habitats had significantly more N. girardi than the others (p<0.01), whereas midchannel habitats were used significantly less often than other habitat types. A greater number of individuals were found in microhabitats defined by depths of 0–50cm and current speeds of 0–50cms^-1 although faster current speeds were used with high frequency. Selection of deeper water was only apparent during the summer. Juveniles selected shallow, slow flowing backwater habitat types more frequently than did adults. Habitats adjacent to underwater sand ridges were important to both adults and juveniles, but similar types such as islands and banks also were used. No single physicochemical feature was linked to high densities of this species. During its life cycle, N. girardi used most of the range of features encountered in the S. Canadian River; thus, maintenance of the riverine landscape (i.e. all of the attributes of rivers in the native range of N. girardi) will be necessary to ensure that this species has access to appropriate habitat types throughout its life cycle.     

Comparative computational analysis of prion proteins reveals two fragments with unusual structural properties and a pattern of increase in hydrophobicity associated with disease-promoting mutations

Prion diseases are a group of neurodegenerative disorders associated with conversion of a normal prion protein, PrPC, into a pathogenic conformation, PrPSc. The PrPSc is thought to promote the conversion of PrPC. The structure and stability of PrPC are well characterized, whereas little is known about the structure of PrPSc, what parts of PrPC undergo conformational transition, or how mutations facilitate this transition. We use a computational knowledge-based approach to analyze the intrinsic structural propensities of the C-terminal domain of PrP and gain insights into possible mechanisms of structural conversion. We compare the properties of PrP sequences to those of a PrP paralog, Doppel, and to the distributions of structural propensities observed in known protein structures from the Protein Data Bank. We show that the prion protein contains at least two sequence fragments with highly unusual intrinsic propensities, PrP(114-125) and helix B. No segments with unusual properties were found in Doppel protein, which is topologically identical to PrP but does not undergo structural rearrangements. Known disease-promoting PrP mutations form a statistically significant cluster in the region comprising helices B and C. Due to their unusual properties, PrP(114-125) and the C terminus of helix B may be considered as primary candidates for sites involved in conformational transition from PrPC to PrPSc. The results of our study also show that most PrP mutations associated with neurodegenerative disorders increase local hydrophobicity. We suggest that the observed increase in hydrophobicity may facilitate PrP-to-PrP or/and PrP-to-cofactor interactions, and thus promote structural conversion.     

An Analysis of the Amino Acid Clustering Pattern in (α/β)8 Barrel Proteins

The (/)₈ barrel proteins, in spite of having a common fold, do not show any sequence similarity. In order to understand the factors which are responsible for maintaining the common fold, the three-dimensional structures of 36 (/)₈ barrel proteins are analyzed for the presence of identical amino acid clusters or physicochemically similar clusters. The results reveal 14 identical amino acid clusters and a large number of physicochemically similar clusters. Further analysis of the similar clusters points to the conservation of secondary structures, the presence of pairs of residues occupying topologically equivalent secondary structures, and the presence of certain key residues which may play a vital role in directing and stabilizing the (/)₈ barrel fold.     

Environmental and biological factors influence the relationship between a predator fish,Gambusia holbrooki,and its main prey in rice fields of the Lower Mondego River Valley (Portugal)

We studied the relationships between a predator fish, Gambusia holbrooki, and its main food prey, within the content of a rice field food web. The influence of some environmental and biological factors on these trophic interactions, in combination with existent quantitative information, allowed us to evaluate the ecological viability of using a non-ionic surfactant, Genapol OXD-080, to control a plague caused by crayfish (Procambarus clarkii) populations in the rice fields. In the Lower Mondego River Valley, Portugal, G. holbrooki is abundant in rice fields. It feeds mainly on copepods, cladocerans and rotifers. Surface insects, such as aphids, collembolans, adult (imago) chironomids and other dipterans, are additional food. Large G. holbrooki consumed greater amounts of cladocerans and adult chironomids than other smaller size groups, while small fish prefered rotifers. Gravid females ate copepods, cladocerans, and adult chironomids and other dipterans in significantly greater amounts than immatures, males, and non-gravid females. Non-gravid females ate collembolans in significantly greater quantities than any other fish group. The population density of copepods, cladocerans, adult chironomids, and other dipterans, the area covered by aquatic vegetation, and water temperature all had significant effects on the total number of prey caught by G. holbrooki. In contrast, a negative correlation was found with rotifers, collembolans, aphids in higher densities, and of increased water volume, dissolved oxygen and pH. G. holbrooki holds a key intermediate position in the rice field food chain, feeding in large amounts of aquatic invertebrates and being eaten, in turn, by piscivores. With regard to the toxicity of Genapol OXD-080 on non-target organisms, LC₅₀ values for G. holbrooki and some of its main prey were several times lower than the concentration necessary to decrease the activity of crayfish populations in the rice fields. Thus, Genapol OXD-080 could potentially cause greater damage to the local populations of non-target species and should not be used without taking precautions not to contaminate other important biological reservoirs, such as the rice field irrigation channels. This revised version was published online in July 2006 with corrections to the Cover Date.     

Relationships between height and girth of mangroves and soil-water conditions in the Mary and Hawkesbury River estuaries,eastern Australia

Abstract The height and diameter at breast height (DBH) of mangroves on the Hawkesbury River, New South Wales and the Mary River, Queensland were related to soil-water salinity, soil-water content and distance from the mouth of the estuary. On the Hawkesbury River, both Avicennia marina and Aegiceras corniculatum declined in height and DBH with increasing soil-water salinity and soil-water content, and increased in height with distance from the mouth of the estuary. Both species showed an extensive range of all variables. On the Mary River, where species diversity was higher, no relationship was found between the height and DBH of A. marina and A. corniculatum and soil-water salinity and soil-water content. Both species increased in height with increasing distance from the mouth of the estuary, a characteristic shared with all other species studied (Excoecaria agallocha, Ceriops tagal var. australis, Rhizophora stylosa). The results suggest that growth characteristics of mangroves are not a simple response to salinity gradients in diverse systems and that other variables such as nutrient availability may be important controls on mangrove growth.     

Comparison of substrate utilization and growth kinetics between immobilized and suspended Pseudomonas cells

A methodology is described for measurement if immobilized and suspended cell growth and substrate utilization kinetics parameters. Substrate utilization and growth kinetics were compared between immobilized and suspended cells for toluene degrading Pseudomonas strains K3-2 and 2,4-dichlorophenoxyacetic acid (2,4-D) degrading strain DBO131(pR0101), respectively. Kinetic parameters were estimated using nonlinear parameter estimation methods and compared between the immobilized and suspended Pseudomonas cells to determine the effect of immobilization on cellular growth and substrate utilization. Factors influencing the experimental design included calculated oxygen flux rates, primary carbon substrate flux rates, and shear stresses on the immobilize cell. Statistical interpretation of the cellular reaction rate parameters indicates that only the growth kinetics of the toluene system were significantly altered upon immobilization. Substrate utilization kinetics remained unchanged upon immobilization. The substrate growth associated half-saturation constant (K(g)) for the toluene system increased by 30-fold and the maximum specific growth rate (mu(max)) decreased by 2-fold upon immobilization. Implication of these results for experimental determination of cellular kinetic parameters and for immobilization cell bioreactors design are discussed. (c) 1993 John Wiley & Sons, Inc.