Plant mRNA 3′-end formation

Our understanding of how the 3 ends of mRNAs are formed in plants is rudimentary compared to what we know about this process in other eukaryotes. The salient features of plant pre-mRNAs that signal cleavage and polyadenylation remain obscure, and the biochemical mechanism is as yet wholly uncharacterised. Nevertheless, despite the lack of universally conserved cis-acting motifs, a common underlying architecture is emerging from functional analyses of plant poly(A) signals, allowing meaningful comparison with components of poly(A) signals in other eukaryotes. A plant poly(A) signal consists of one or more near-upstream elements (NUE), each directing processing at a poly(A) site a short distance downstream of it, and an extensive far-upstream element (FUE) that enhances processing efficiency at all sites. By analogy with other systems, a model for a plant 3-end processing complex can be proposed. Plant poly(A) polymerases have been isolated and partially characterised. These, together with hints that some processing factors are conserved in different organisms, opens promising avenues toward initial characterisation of the trans-acting factors involved in 3-end formation of mRNAs in higher plants.     

Trophic Levels and Functional Feeding Groups of Macroinvertebrates in Neotropical Streams

Feeding strategies are typical traits reflecting the adaptation of species to environmental conditions. This concept is currently developed in some water quality systems (e.g. Index of Trophic completeness) and the structure of functional feeding groups (FFGs) could form part of a unified measure across communities differing in taxonomic composition. However, in South America, information about the FFG classification of invertebrates in streams is almost absent and existing studies using FFG structure follows classification from North America. But even taxonomically related species may have different diets in tropical and temperate areas and therefore, studies about FFG structure in neotropics could be biased. For this reason, we determined diet composition, trophic level and FFGs, using gut contents analysis and mouthpart observations of 49 macroinvertebrate taxa (mostly at genus level) from neotropical streams. We observed that practically all macroinvertebrates fed upon fine detritus which indicates the importance of this food resource in neotropical streams. As the assignment to a single FFG does not accurately reflect the functional profile of taxa, we transcribed the affinity of taxa to each FFG using fuzzy codes. Finally, we published the coding of diet composition and FFG of the taxa examined, which could be used in future community analyses of lotic ecosystems in the Neotropical zone.     

The heterotopic tracheal allograft as an animal model of obliterative bronchiolitis

Heterotopic tracheal allografts in small rodents have been shown to share many characteristics with the development of obliterative bronchiolitis (OB) in the clinic and therefore provide a suitable animal model for the study of OB. The model facilitates the examination of the pathogenesis of the disease and the elucidation of the cellular and molecular mechanisms involved in its development. The model provides a less technically demanding alternative to whole lung transplantation in small rodents and should lead to a speedier identification of new treatments that might prevent the development of post-transplantation OB in the clinic.     

First Siena International Conference on Animal Models of Chronic Obstructive Pulmonary Disease, Certosa di Pontignano, University of Siena, Italy, September 30-October 2, 2001

The meeting proved of great interest to those developing an animal model of chronic obstructive pulmonary disease (COPD). COPD is caused by cigarette smoking, evidenced by deterioration in lung function. Lung function is only rarely assessed in animal models. A cigarette smoke driven pathology should provide the best in vivo model for COPD. However, as lesions produced this way take 8–12 months to develop other strategies have to be employed. Emphysematous lesions were also achieved by treatment with elastase, lipopolysaccharide, ozone and other inducers. Several studies described treatments that have shown activity in these models. Transgenic models were discussed, as was the importance of species and strain selection.     

Environmental impact of heated mining waters on clitellate (Annelida: Clitellata) assemblages

Mining is a relatively highly monitored industry. While chemical pollutants (toxic ions, radionuclides, etc.) have mostly been eliminated from mining waters, other types of environmental pollution (temperature regime alterations, high concentrations of various anions, etc.) can affect benthic invertebrates. In this study, we focused on the effect of mining water effluent on the diversity and density of aquatic Clitellata. Four sampling sites were selected. Three sites in a natural stream (the Nedvědi?ka River, Czech Republic), one upstream and two downstream from the mining effluent, and one site on the mining waters were sampled monthly during 2008–2009. Environmental variables were recorded in and samples were collected from two types of habitats — riffles and pools. The response of clitellate assemblages was evaluated using principal component analysis and generalised estimating equations. The results indicated that the mining effluent caused partial species exchange and had negative effects on clitellate taxa richness and abundance. These responses were specific to both the habitat (riffle/pool) and species sampled. In each of the different taxa studied, we observed one of four typical clitellate responses: (a) elimination of stenotherm species; (b) reduction of clitellate species followed by quick recovery; (c) neutral response; or (d) positive influence. We found that aquatic clitellates, which are considered to be eurytopic with broad ecological valences, are also sensitive to even slight environmental pollution.     

The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation

The International Mouse Phenotyping Consortium (IMPC) is building a catalogue of mammalian gene function by producing and phenotyping a knockout mouse line for every protein-coding gene. To date, the IMPC has generated and characterised 5186 mutant lines. One-third of the lines have been found to be non-viable and over 300 new mouse models of human disease have been identified thus far. While current bioinformatics efforts are focused on translating results to better understand human disease processes, IMPC data also aids understanding genetic function and processes in other species. Here we show, using gorilla genomic data, how genes essential to development in mice can be used to help assess the potentially deleterious impact of gene variants in other species. This type of analyses could be used to select optimal breeders in endangered species to maintain or increase fitness and avoid variants associated to impaired-health phenotypes or loss-of-function mutations in genes of critical importance. We also show, using selected examples from various mammal species, how IMPC data can aid in the identification of candidate genes for studying a condition of interest, deliver information about the mechanisms involved, or support predictions for the function of genes that may play a role in adaptation. With genotyping costs decreasing and the continued improvements of bioinformatics tools, the analyses we demonstrate can be routinely applied.     

Seasonal dynamics of Bythonomus lemani and Bothrioneurum vejdovskyanum (Oligochaeta, Annelida) in relation to environmental variables

The seasonal dynamics of Bythonomus lemani (Lumbriculidae) were studied for the first time and the knowledge of Bothrioneurum vejdovskyanum (Tubificidae) was extended based on four quantitative samples of oligochaetes taken monthly in the Rokytná River (Czech Republic) during a two-year study (April 1999–April 2001). The influence of water temperature, velocity, depth, discharge, pH, conductivity, dissolved oxygen amount and biochemical oxygen demand (BOD) on their life cycles was evaluated. Habitat preferences of the juvenile and adult stages were recorded. Time series analysis was used to determine the worm densities, seasonality and trends. For Byth. lemani one distinct reproduction cycle per year was found and this was regulated by temperature, while Both. vejdovskyanum showed a one-year cycle not significantly dependent on measured environmental variables. The overall trend was an increase in density for Byth. lemani and a decrease in density for Both. vejdovskyanum. Byth. lemani showed a significant negative correlation between the trend of its density and BOD concentration.     

Endo-exo Synergism in Cellulose Hydrolysis Revisited

Synergistic cooperation of different enzymes is a prerequisite for efficient degradation of cellulose. The conventional mechanistic interpretation of the synergism between randomly acting endoglucanases (EGs) and chain end-specific processive cellobiohydrolases (CBHs) is that EG-generated new chain ends on cellulose surface serve as starting points for CBHs. Here we studied the hydrolysis of bacterial cellulose (BC) by CBH TrCel7A and EG TrCel5A from Trichoderma reesei under both single-turnover and "steady state" conditions. Unaccountable by conventional interpretation, the presence of EG increased the rate constant of TrCel7A-catalyzed hydrolysis of BC in steady state. At optimal enzyme/substrate ratios, the "steady state" rate of synergistic hydrolysis became limited by the velocity of processive movement of TrCel7A on BC. A processivity value of 66 ± 7 cellobiose units measured for TrCel7A on (14)C-labeled BC was close to the leveling off degree of polymerization of BC, suggesting that TrCel7A cannot pass through the amorphous regions on BC and stalls. We propose a mechanism of endo-exo synergism whereby the degradation of amorphous regions by EG avoids the stalling of TrCel7A and leads to its accelerated recruitment. Hydrolysis of pretreated wheat straw suggested that this mechanism of synergism is operative also in the degradation of lignocellulose. Although both mechanisms of synergism are used in parallel, the contribution of conventional mechanism is significant only at high enzyme/substrate ratios.