Trophic and individual efficiencies of size-structured communities

Individual and trophic efficiencies of size-structured communities are derived from mechanistically based principles at the individual level. The derivations are relevant for communities with a size-based trophic structure, i.e. where trophic level is strongly correlated with individual size as in many aquatic systems. The derivations are used to link Lindeman's trophic theory and trophic theory based on average individuals with explicit individual-level size spectrum theory. The trophic efficiency based on the transfer of mass between trophic levels through predator-prey interactions is demonstrated to be valid only when somatic growth can be ignored. Taking somatic growth into account yields an average individual growth efficiency that is smaller than the trophic efficiency.     

Screening for cellulose and hemicellulose degrading enzymes from the fungal genus Ulocladium

The fungal genus Ulocladium consists mostly of saprotrophic species and can readily be isolated from dead vegetation, rotten wood, paper, textiles and other cellulose containing materials. Thus, they must produce cellulolytic and hemicellulolytic enzymes. In this study fifty Ulocladium strains from ten different species were tested for enzyme activities on 14 different azurine-cross-linked (AZCL) substrates and analyzed by multivariate analysis. The tested strains of Ulocladium were found to produce a broad enzyme profile. Most species in Ulocladium were able to produced high amounts of enzymes that degraded amylose, arabinoxylan, β-glucan, cellulose and xylan; however, variations between species as well as between individual strains in each species were seen. Overall, the enzyme profiles were found to be species specific, but also source of isolation impacted the enzymes produced. The results suggest that species identity as well as isolation source must be considered when screening microorganisms for enzymes.     

Pro-interleukin (IL)-1�� Shares a Core Region of Stability as Compared with Mature IL-1�� While Maintaining a Distinctly Different Configurational Landscape: A COMPARATIVE HYDROGEN/DEUTERIUM EXCHANGE MASS SPECTROMETRY STUDY*

Interleukin-1β (IL-1β) is a master cytokine involved in initiating the innate immune response in vertebrates (Dinarello, C. A. (1994) FASEB J. 8, 1314–1325). It is first synthesized as an inactive 269-residue precursor (pro-interleukin-1β or pro-IL-1β). Pro-IL-1β requires processing by caspase-1 to generate the active, mature 153-residue cytokine. In this study, we combined hydrogen/deuterium exchange mass spectrometry, circular dichroism spectroscopy, and enzymatic digestion comparative studies to investigate the configurational landscape of pro-IL-1β and the role the N terminus plays in modulating the landscape. We find that the N terminus keeps pro-IL-1β in a protease-labile state while maintaining a core region of stability in the C-terminal region, the eventual mature protein. In mature IL-1β, this highly protected region maps back to the area protected earliest in the NMR studies characterizing an on-route kinetic refolding intermediate. This protected region also encompasses two important functional loops that participate in the IL-1β/receptor binding interface required for biological activity. We propose that the purpose of the N-terminal precursor region in pro-IL-1β is to suppress the function of the eventual mature region while keeping a structurally and also functionally important core region primed for the final folding into the native, active state of the mature protein. The presence of the self-inhibiting precursor region provides yet another layer of regulation in the life cycle of this important cytokine.Nearly all cell types respond to interleukin (IL)-1β,⁴ in a very sensitive manner, via binding to the interleukin-1 receptor type 1 (IL-1RI) (2). Although essential in the immune response, overproduction of IL-1β can lead to both acute (sepsis) as well as chronic (rheumatoid arthritis, atherosclerosis, obesity, and diabetes) disease states (3). Thus, the expression, activation, and secretion of this cytokine are tightly controlled (4). Although many cell types express IL-1β, it is predominately produced and secreted by monocytes and macrophages (1). The protein is synthesized as a biologically inactive 269-residue precursor molecule, pro-interleukin-1β (pro-IL-1β), and the 153-residue active mature IL-1β is generated from the C-terminal domain. Processing of the proprotein involves the recently discovered NALP-1 and NALP-3 inflammasomes, which are responsible for activating procaspase-1 (5). The inflammasome function is integral in wound repair as well as for combating infection (6–9).In vivo, the 31-kDa pro-IL-1β precursor is processed to the active C-terminal 17-kDa form by the interleukin-1 converting enzyme, caspase-1 (10, 11). Caspase-1 is a cysteine protease that recognizes two cleavage sites in pro-IL-1β, the Asp²⁷↓Gly²⁸ and Asp¹¹⁶↓Ala¹¹⁷ peptide bonds (Fig. 1A). These cleavage sites are conserved across mammals (12–14). The activation pathway is believed to proceed with cleavage first at Asp²⁷↓Gly²⁸ (site 1) followed by Asp¹¹⁶↓Ala¹¹⁷ (site 2). These processing events lead to the generation of the mature, active IL-1β from the C-terminal domain of pro-IL-1β (15). After cleavage, the mature protein is exported via a cell-specific non-classical pathway (16). The events leading from caspase-1 activation to active IL-1β secretion are poorly understood and constitute an area of active research (16–20).Open in a separate windowFIGURE 1.A, a schematic of pro-interleukin-1β processing by caspase-1. The two caspase-1 cleavage sites are labeled by residue/number. The products for the cleavage scenario are represented as smaller blocks, and the final mature protein as the actual three-dimensional structure shown in blue (Protein Data Bank code 6I1B (74)). B, panel i, important features are highlighted on the structure of mature IL-1β. Residues Tyr⁶⁸ (residue 184 in pro-IL-1β) and Trp¹²⁰ (236 in pro-IL-1β) are indicated by red side chain stick representation. The two loops important for binding at the third Ig domain of the receptor are indicated by blue spheres (the basic/hydrophobic 90s loop, which encompasses residues 85–99 in mature and 201–216 in pro-IL-1β) and yellow spheres (the β-bulge, residues 46–53 and 162–169). The numbering corresponds to mature and pro-IL-1β, respectively. Panel ii, after rotating the structure 90°, the individual trefoils are labeled by color (trefoil 1 in orange, trefoil 2 in yellow, and trefoil 3 in blue). The structural features described in panel i maintain the same coloring. Panel iii, the two-dimensional splay diagram of the trefoils labeled by color as in panel ii showing the 3-fold symmetry of the secondary structure elements.The native structure of IL-1β is classified as a β-trefoil. The global protein-fold contains three pseudo-symmetric βββloopβ motifs that coalesce to form a six-stranded barrel with three hairpins that form a six-stranded cap closing one end of the barrel (see Fig. 1B) (21). Mature IL-1β refolds relatively slowly (22), accessing multiple routes including a major route with a detectable intermediate population (23, 24). Recently, this slow folding has been attributed to repacking of a functionally important loop (the β-bulge) in the mature protein (see Fig. 1B, i) (25–27). Although much information is known about the structure, folding, and function of mature IL-1β, there is little information available on pro-IL-1β, despite the central importance of this molecule in mediating critical inflammatory processes (28–30). What is known is that the presence of the N-terminal 116 amino acids results in a highly protease-sensitive protein with no biological activity (31). Folding of mature IL-1β is believed to occur after cleavage of pro-IL-1β in vivo. Therefore, structural analysis of the precursor is essential for a better understanding of the role the precursor region plays in regulating folding events leading to the generation of the eventual mature protein.The crystal structure of pro-IL-1β has not been determined, despite approximately 25 years of intensive efforts directed toward this goal, as a result of the dynamic nature of this molecule (32–34). Therefore, we used structure-sensitive methods to compare pro-IL-1β in reference to the mature protein. Optical methods in combination with hydrogen/deuterium exchange mass spectrometric analysis (DXMS) and enzymatic digestion were used to investigate how the N-terminal precursor region modulates the properties of the C-terminal mature domain. DXMS is a well established technique for characterizing proteins refractory to standard crystallographic or NMR structure determination techniques (35–37). Taken together, our results indicate that the N terminus inhibits folding to the fully active trefoil structure in the C-terminal region, but maintains the protein in a conformation that is primed for efficient folding upon release after caspase-1 cleavage.     

Feeding,resting and social behaviour in ewes housed in two different group sizes

The aim of this experiment was to investigate the effects of increased group size on eating- and resting behaviour, aggression and feed intake in housed ewes. During an initial period of 14 days 36 adult (2–6 years old) ewes of the domestic Norwegian Dala breed were divided into four groups of 9. In the second period (14 days), these ewes were merged into one group of 36 ewes. This experiment was repeated with a second batch of ewes, but this time starting with a group of 36 individuals in the first period, then splitting them up into four groups of 9 ewes in the second period. From 24 h video recordings we scored activity behaviours using instantaneous sampling every 10 min. Aggressive interactions were continuously observed the first 10 min every hour during the 24 h (4 h in total). A mixed statistical procedure with group size, day, batch and the interactions between them were included as fixed effects, whereas individual and group were specified as random effects.Ewes in large groups (36) had a larger variation in lying time at day one (P < 0.01), less synchronized lying (P < 0.05) and eating behaviour (P < 0.01), and spent less time queuing at the feed barrier (P < 0.001) compared to in the small group size (9). There were no effects of group size on aggressive interactions or feed intake.In conclusion, a larger group size decreased synchrony in resting and feeding behaviour and reduced the time spent queuing in front of the feed barrier. It is possible that the aggression level in sheep is more sensitive to changes in space allowance than to changes in group size per se.     

Who wants to live forever? Roe deer survival in a favourable environment

The survival rates and body masses of roe deer (Capreolus capreolus) were studied on the island of Storfosna in central Norway in relation to sex, age, season and year. There were no predators on the island, and hunting was halted during the study period, resulting in a population increase from 10 to 40 individuals per km² during the period 1991–1994. A total of 352 individual roe deer were radio-monitored on a monthly basis. Survival rates were analyzed using the MARK software. An age effect in survival was found separating fawns from yearlings and adults, and for yearlings and adults we furthermore found a year effect. There was evidence for density dependence in body masses of fawns and yearlings, but no density effect in survival rates. We found no sex effect in winter body mass, but a significant sex effect in survival rates. We conclude that (1) increased population density can have an effect on body masses without causing a change in survival rates (2) roe deer can maintain very high survival rates under favourable environmental conditions even at very high population densities (3) male adults can reach equally high survival rates as females under favourable circumstances.     

Potent inhibitors of Huntingtin protein aggregation in a cell-based assay

A quinazoline that decreases polyglutamine aggregate burden in a cell-based assay was identified from a high-throughput screen of a chemical-compound library, provided by the NIH Molecular Libraries Small Molecule Repository (MLSMR). A structure and activity study yielded leads with submicromolar potency.     

Stable intermediates determine proteins' primary unfolding sites in the presence of surfactants

Despite detailed knowledge of the overall structural changes and stoichiometries of surfactant binding, little is known about which protein regions constitute the preferred sites of attack for initial unfolding. Here we have exposed three proteins to limited proteolysis at anionic (SDS) and cationic (DTAC) surfactant concentrations corresponding to specific conformational transitions, using the surfactant‐robust broad‐specificity proteases Savinase and Alcalase. Cleavage sites are identified by SDS‐PAGE and N‐terminal sequencing. We observe well‐defined cleavage fragments, which suggest that flexibility is limited to certain regions of the protein. Cleavage sites for α‐lactalbumin and myoglobin correspond to regions identified in other studies as partially unfolded at low pH or in the presence of organic solvents. For Tnfn3, which does not form partially folded structures under other conditions, cleavage sites can be rationalized from the structure of the protein's folding transition state and the position of loops in the native state. Nevertheless, they are more sensitive to choice of surfactant and protease, probably reflecting a heterogeneous and fluctuating ensemble of partially unfolded structures. Thus, for proteins accumulating stable intermediates on the folding pathway, surfactants encourage the formation of these states, while the situation is more complex for proteins that do not form these intermediates. © 2008 Wiley Periodicals, Inc. Biopolymers 91: 221–231, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com