Phage display and structural studies reveal plasticity in substrate specificity of caspase‐3a from zebrafish

The regulation of caspase‐3 enzyme activity is a vital process in cell fate decisions leading to cell differentiation and tissue development or to apoptosis. The zebrafish, Danio rerio, has become an increasingly popular animal model to study several human diseases because of their transparent embryos, short reproductive cycles, and ease of drug administration. While apoptosis is an evolutionarily conserved process in metazoans, little is known about caspases from zebrafish, particularly regarding substrate specificity and allosteric regulation compared to the human caspases. We cloned zebrafish caspase‐3a (casp3a) and examined substrate specificity of the recombinant protein, Casp3a, compared to human caspase‐3 (CASP3) by utilizing M13 bacteriophage substrate libraries that incorporated either random amino acids at P5‐P1′ or aspartate fixed at P1. The results show a preference for the tetrapeptide sequence DNLD for both enzymes, but the P4 position of zebrafish Casp3a also accommodates valine equally well. We determined the structure of zebrafish Casp3a to 2.28Å resolution by X‐ray crystallography, and when combined with molecular dynamics simulations, the results suggest that a limited number of amino acid substitutions near the active site result in plasticity of the S4 sub‐site by increasing flexibility of one active site loop and by affecting hydrogen‐bonding with substrate. The data show that zebrafish Casp3a exhibits a broader substrate portfolio, suggesting overlap with the functions of caspase‐6 in zebrafish development.     

Organic mulches in highbush blueberries alter beetle (Coleoptera) community composition and improve functional group abundance and diversity

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The migration game in habitat network: the case of tuna

Long-distance migration is a widespread process evolved independently in several animal groups in terrestrial and marine ecosystems. Many factors contribute to the migration process and of primary importance are intra-specific competition and seasonality in the resource distribution. Adaptive migration in direction of increasing fitness should lead to the ideal free distribution (IFD) which is the evolutionary stable strategy of the habitat selection game. We introduce a migration game which focuses on migrating dynamics leading to the IFD for age-structured populations and in time varying habitats, where dispersal is costly. The model predicts migration dynamics between these habitats and the corresponding population distribution. When applied to Atlantic bluefin tunas, it predicts their migration routes and their seasonal distribution. The largest biomass is located in the spawning areas which have also the largest diversity in the age-structure. Distant feeding areas are occupied on a seasonal base and often by larger individuals, in agreement with empirical observations. Moreover, we show that only a selected number of migratory routes emerge as those effectively used by tunas.     

Neodymium yttrium aluminium garnet laser photocoagulation for major haemorrhage from peptic ulcers and single vessels: a single blind controlled study.

A prospective single blind controlled trial was performed to assess the efficacy of the neodymium yttrium aluminium garnet laser in the management of patients bleeding from peptic ulcers and single vessels. Over 20 months 184 patients were found at endoscopy to be bleeding from peptic ulcers and single vessels; 130 of these failed to meet the criteria for entry into the study, but their bleeding stopped with conservative management. Forty-five patients entered the study: in all 25 who were bleeding from ulcers with spots the bleeding stopped irrespective of the treatment allocated. Twenty patients were bleeding from arteries. Eight were allocated to placebo treatment, and all later underwent emergency surgery for further haemorrhage. Twelve were allocated to receive laser treatment, and only one of eight who actually received it required surgery (p less than 0.002). It is concluded that laser treatment reduces the incidence of further haemorrhage and the need for emergency surgery, but the technique is difficult and not always applicable.     

Formiminotransferase-cyclodeaminase from procine liver. Purification and physical properties of the enzyme complex.

A simple procedure for the purification of the formiminotransferase-cyclodeaminase enzyme complex is described. The crystalline preparation is homogeneous by ultracentrifugation and electrophoresis and appears to be composed of eight apparently identical subunits of about 6.4 × 10⁴ daltons. Both enzyme activities migrate with the single protein band on electrophoresis and it is proposed that the activities are probably associated with different sites on one type of polypeptide chain.     

Some aspects of the biology of the cercaria and metacercaria of Stephanostomum baccatum (Nicoll, 1907) Manter, 1934 (Digenea: Acanthocolpidae)

Experimental proof is presented that Cercaria neptunae Lebour is the cercaria of Stephanostomum baccatum and that the gastropods Buccinum undatum (L.) and Neptunea antiqua (L.) both act as its first intermediate hosts in the north-east Atlantic. Heavy experimental infections were associated with mortalities of 0+plaice Pleuronectes platessa (L.). The probable effects on plaice of infections at intensities below the lethal level are discussed. Under natural conditions almost all S. baccatum infection of plaice occurs in the first year of life, but newly emerged cercariae were shown experimentally to be capable of encysting in the musculature of plaice up to three years old. The thicker epidermis of older plaice may account for their resistance to infection. Common dabs were more easily infected than plaice. The ability of S. baccatum cercariae to infect plaice and common dabs is inversely related to the length of time between emergence and contact with the host. The differences in skin structure between opposite sides of the plaice body may account for the asymmetrical distribution of metacercariae in the musculature. The potential use of S. baccatum as a biological tag is discussed.     

Fermentation of xylose and hemicellulose hydrolysates by an ethanol-adapted culture ofBacteroides polypragmatus

Bacteroides polypragmatus type strain GP4 was adapted to grow in the presence of 3.5% (w/v) ethanol by successive transfers into 1% (w/v)d-xylose media supplemented with increasing concentrations of ethanol. The maximum specific growth rate of the ethanol-adapted culture (=0.30 h^-1) was not affected by up to 2% (w/v) ethanol but that of the non-adapted strain declined by about 50%. The growth rate of both cultures was limited by nutrient(s) contained in yeast extract. The ethanol yield of the adapted culture (1.01 mol/mol xylose) was higher than that (0.80 mol/mol xylose) of the non-adapted strain. The adapted culture retained the ability to simultaneously ferment pentose and hexose sugars, and moreover it was not inhibited by xylose concentrations of 7–9% (w/v). This culture also readily fermented hemicellulose hydrolysates obtained by mild acid hydrolysis of either hydrogen fluoride treated or steam exploded Aspen wood. The ethanol yield from the fermentation of the hydrolysates was comparable to that obtained from xylose.This paper is issued as NRCC No. 26338     

Further studies on a hybrid cell-surface antigen associated with human chromosome 11 using a monoclonal antibody

A monoclonal antibody has been obtained that recognizes an antigen encoded by human chromosome 11. We present evidence that this monoclonal antibody recognizes the same or a similar antigenic activity as that previously called a1. Genetic information necessary for a1 expression and recognition by the monoclonal antibody both map to 11p13 leads to 11pter. Mutants that have lost a1 are no longer recognized by the monoclonal antibody. The macroglycolipid fraction of human erythrocyte membranes which contains the a1 antigenic activity is able to convert antigen-negative Chinese hamster ovary cells into cells which are killed by the monoclonal antibody plus complement.