Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme

Mechanical unfolding trajectories for single molecules of the Tetrahymena thermophila ribozyme display eight intermediates corresponding to discrete kinetic barriers that oppose mechanical unfolding with lifetimes of seconds and rupture forces between 10 and 30 piconewtons. Barriers are magnesium dependent and correspond to known intra- and interdomain interactions. Several barrier structures are "brittle," breakage requiring high forces but small (1 to 3 nanometers) deformations. Barrier crossing is stochastic, leading to variable unfolding paths. The response of complex RNA structures to locally applied mechanical forces may be analogous to the responses of RNA during translation, messenger RNA export from the nucleus, and viral replication.     

C-cadherin ectodomain structure and implications for cell adhesion mechanisms

Cadherins are transmembrane proteins that mediate adhesion between cells in the solid tissues of animals. Here we present the 3.1 angstrom resolution crystal structure of the whole, functional extracellular domain from C-cadherin, a representative "classical" cadherin. The structure suggests a molecular mechanism for adhesion between cells by classical cadherins, and it provides a new framework for understanding both cis (same cell) and trans (juxtaposed cell) cadherin interactions. The trans adhesive interface is a twofold symmetric interaction defined by a conserved tryptophan side chain at the membrane-distal end of a cadherin molecule from one cell, which inserts into a hydrophobic pocket at the membrane-distal end of a cadherin molecule from the opposing cell.     

Droplet infiltration and organic matter composition of intact crack and biopore surfaces from clay‐illuvial horizons

The organic matter (OM) in biopore walls and aggregate coatings may be important for sorption of reactive solutes and water as well as for solute mass exchange between the soil matrix and the preferential flow (PF) domains in structured soil. Structural surfaces are coated by illuvial clay‐organic material and by OM of different origin, e.g., earthworm casts and root residues. The objectives were to verify the effect of OM on wettability and infiltration of intact structural surfaces in clay‐illuvial horizons (Bt) of Luvisols and to investigate the relevance of the mm‐scale distribution of OM composition on the water and solute transfer. Intact aggregate surfaces and biopore walls were prepared from Bt horizons of Luvisols developed from Loess and glacial till. The mm‐scale spatial distribution of OM composition was scanned using diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy. The ratio between alkyl and carboxyl functional groups in OM was used as potential wettability index (PWI) of the OM. The infiltration dynamics of water and ethanol droplets were determined measuring contact angles (CA) and water drop penetration times (WDPT). At intact surfaces of earthworm burrows and coated cracks of the Loess‐Bt, the potential wettability of the OM was significantly reduced compared to the uncoated matrix. These data corresponded to increased WDPT, indicating a mm‐scaled sub‐critical water repellency. The relation was highly linear for earthworm burrows and crack coatings from the Loess‐Bt with WDPT > 2.5 s. Other surfaces of the Loess‐Bt and most surfaces of the till‐derived Bt were not found to be repellent. At these surfaces, no relations between the potential wettability of the OM and the actual wettability of the surface were found. The results suggest that water absorption at intact surface structures, i.e., mass exchange between PF paths and soil matrix, can be locally affected by a mm‐scale OM distribution if OM is of increased content and is enriched in alkyl functional groups. For such surfaces, the relation between potential and actual wettability provides the possibility to evaluate the mm‐scale spatial distribution of wettability and sorption and mass exchange from DRIFT spectroscopic scanning.     

Population structure and virulence content of avian pathogenic Escherichia coli isolated from outbreaks in Sri Lanka

Avian pathogenic Escherichia coli (APEC) causes economically significant infections in poultry. The genetic diversity of APEC and phylogenetic relationships within and between APEC and other pathogenic E. coli are not yet well understood. We used multilocus sequence typing (MLST), PCR-based phylogrouping and virulence genotyping to analyse 75 avian E. coli strains, including 55 isolated from outbreaks of colisepticaemia and 20 from healthy chickens. Isolates were collected from 42 commercial layer and broiler chicken farms in Sri Lanka. MLST identified 61 sequence types (ST) with 44 being novel. The most frequent ST, ST48, was represented by only six isolates followed by ST117 with four isolates. Phylogenetic clusters based on MLST sequences were mostly comparable to phylogrouping by PCR and MLST further differentiated phylogroups B1 and D into two subgroups. Genotyping of 16 APEC associated virulence genes found that 27 of the clinical isolates and one isolate from a healthy chicken belonged to highly virulent genotype according to previously established classification schemes. We found that a combination of four genes, ompT, hlyF, iroN and papC, gave a comparable prediction to that of using five and nine genes by other studies. Four STs (ST10, ST48, ST117 and ST2016) contained APEC isolates from this study and human UPEC isolates reported by others, suggesting that these STs are potentially zoonotic. Our results enhanced the understanding of APEC population structure and virulence association.     

Species‐specific distribution model may be not enough: The case study of bottlenose dolphin (Tursiops truncatus) habitat distribution in Pelagos Sanctuary

1. Geospatial models are used to predict the distribution of terrestrial and marine species, according to their ecological and ethological habits. The bottlenose dolphin is a cosmopolitan marine top predator, inhabiting most of the ocean, with the exception of polar and subpolar waters. This wide distribution is associated with a remarkable plasticity in ecological and behavioural habits, which makes it difficult to model and predict its distribution.
2. This study proposes a ‘multi‐type approach’ to predict the presence and distribution of the bottlenose dolphin in the Pelagos Sanctuary, a Specially Protected Area of Mediterranean Importance located in the north‐west Mediterranean Sea. A multi‐type model based on random forest regression was developed, analysing the distribution habits of two geographical units living in the Pelagos area.
3. When compared with a classical single‐type model, the multi‐type model performed much better in a prediction test (true skill statistics, TSS = 85% vs. 52%), confirming the value of this experimental approach. This work suggests that wild species should not be considered as one single‐type entity, as local specialization may change and shape their distribution habits.

     

Utilization of carotenoids from various sources by rainbow trout: muscle colour,carotenoid digestibility and retention

Rainbow trout (Oncorhynchus mykiss) with a mean (sd) weight of 120 (2) g were fed diets supplemented with astaxanthin extracted from the yeast Phaffia rhodozyma (OY1 = 50 mg carotenoids kg^–1 feed, OY2 = 100 mg carotenoids kg^–1 feed), astaxanthin (AX = 100 mg astaxanthin kg^–1 feed) and canthaxanthin (CX = 100 mg canthaxanthin kg^–1 feed) for 4 weeks. Muscle analyses at the end of the experiment indicated a significantly higher carotenoid concentration in the AX group, while CX and OY1 groups were similar in spite of the differences in dietary concentration. The measure of total muscle colour difference (E^* _ab) between initial samples and 4 week ones was higher for the AX fish group but showed no significant difference between OY1, OY2, and CX. The hue and the reflectance ratio (R₆₅₀:R₅₁₀) of fish muscle increased in proportion to carotenoid intake. Digestibility (ADC) of yeast astaxanthin in OY1 and OY2 groups was significantly higher than that in the AX group. Canthaxanthin ADC was about one sixth of that of astaxanthin (AX group). Carotenoid retention in the muscle, expressed as a percentage of carotenoid intake, was higher for the AX group than that recorded for OY1 and OY2. According to ADC, carotenoid retention showed a marked lower value for the CX group. Muscle retentions were similar for astaxanthins from both sources.     

Measurement of plasma leucine flux in rainbow trout (Salmo gairneri R.) using osmotic pump. Preliminary investigations on influence of diet

A method for the direct measurement of plasma amino acid flux, in rainbow trout, using the continuous infusion of L-[U-¹⁴C]-leucine with ALZET mini-osmotic pumps implanted into the peritoneal cavity, was developed. The fish were fed successively on three different diets (a commercial control diet, a semi-purified diet and a purified diet) during the 4 weeks of experiment. The amounts of radioactivity in the free pool and the protein of both the plasma and skin mucus were measured in these fish. The total flux of leucine was calculated either from the specific activity of leucine in the plasma (61.8 mg leucine. 100 g^-1.d^-1) or from the amounts of labelled and unlabelled leucine flowing into the skin mucus protein (61.5 mg leucine. 100g^-1.day^-1). The total plasma flux was not affected by changes in the diet. The contributions of total leucine oxidation and whole body protein turnover to plasma leucine flux (80% and 20% respectively) were estimated in fish fed the semi-purified diet.     

Impact of four turf management regimes on arthropod abundance in lawns

BACKGROUND: Turfgrass management practices, especially the use of chemical pesticides, may be detrimental to beneficial arthropods such as predators and decomposers. However, little is known about the impact of other practices or pest control products on these beneficials. The impact of four different management regimes, consisting of synthetic pesticide cover sprays or combinations of more targeted applications of natural pesticides, on selected groups of non‐targeted arthropods in lawns of different age was studied over 3 years. The short‐term effect of diazinon and carbaryl on Carabidae and Collembola was also evaluated. RESULTS: Formicidae and Araneae were the most abundant taxa at both sites, representing 74–80% of total captures. With a few short‐term exceptions, no persistent and significant difference between turfgrass management regimes on arthropod abundance was observed over the 3 year study. Diazinon and carbaryl significantly reduced Carabidae abundance, but only one year out of three, while Collembola abundance was only transiently affected by carbaryl application in 2003. CONCLUSION: The study showed that practices and products used in the four management regimes did not disrupt the populations of specific groups of arthropods. These results provide useful information to professionals for the development of ecological turf practices to maintain beneficial arthropod abundance and diversity in urban landscapes. Copyright © 2012 Society of Chemical Industry