The in vitro synthesis and characteristics of ribosomal RNA in imaginal discs of Drosophila melanogaster

Summary Late third instar imaginal discs of Drosophila melanogaster cultured in vitro in Robb's tissue culture medium synthesize 38S, 28S and 18S ribosomal RNAs which are qualitatively indistinguishable from their in vivo synthesized counterparts (Fig. 1). As found in other insect systems, the 38S molecule appears to be the precursor for both the 28S and 18S rRNAs (Figs. 2, 3 and 4). The 28S rRNA and a portion of the 38S pre-rRNA shift in sedimentation value upon exposure to heat or dimethylsulfoxide (Figs. 5 and 8). Studies of the thermal denaturations of these molecules (Figs. 6, 7 and 9) indicate the existence of a single class of 28S rRNA, but three classes of 38S pre-rRNAs. The addition of -ecdysone to the in vitro culture medium stimulates the net amount of rRNA synthesized, increases the rate of processing of the 38S precursor and increases the relative amount of 18S material produced (Figs. 10 and 12).This work was supported in part by grants from the National Science Foundation (GB-8176) and from the Atomic Energy Commission (AT-04-3-34).Predoctoral Trainees, PHS Training Grant No. 2-Tl-GM367 from Research Training Grants Branch, National Institute of General Medical Sciences.1 For purposes of simplification we shall refer to the rRNA molecules of D. melanogaster as being 38S, 30S, 28S and 18S; however, it should be noted that these values are approximate (see Hastings and Kirby, 1966; Greenberg, 1969; Tartof and Perry, 1970).     

Density-dependent decline of breeding success in an introduced, increasing mute swan Cygus olor population

An increasing population of the mute swan Cygnus olor , was studied from its very establishment in 1976 until 1998. As the number of pairs increased, there was a decline in all production parameters, including the average number of clutches per pair, the average number of broods per clutch, and the average number of fledged young per brood. In a multiple regression analysis covering the whole breeding season, the number of pairs and the average number of clutches per pair explained 71% of the variation in the average number of fledglings per pair. During the brood season, the average number of fledglings per brood was an additionally important parameter in explaining fledgling production. Habitat quality seemed to affect breeding: in places occupied earlier more cygnets fledged from a clutch than in habitats inhabited later. The decreased production of young very likely reflects density-dependent effects on reproduction. This density dependence seems to operate on the breeding grounds, since winter harshness did not affect breeding success. Density-dependent processes started acting already when pairs were beginning to nest, and continued during the brood period. Density dependence has apparently not been detected at the pair stage in earlier studies of bird populations.     

Thermodynamical model for insertion and aggregate binding of caffeine to the homopolymer poly(riboadenylate) and model choice by data analysis

This paper describes the model used to estimate the parameters of caffeine-poly(riboadenylate) (poly(A)) interactions from corresponding 1H-NMR measurements. The model of insertion and aggregate binding describes the non-cooperative insertion of a molecule C into an interspace between two monomers of a homopolymer in competition with aggregate binding. It contains two binding constants, K1 for insertion and K2 for the interaction of monomeric A units of the polymer with C molecules in bound aggregates, and two cooperativity parameters, Kcc for stacking of C molecules within aggregates and tau which is thought to be due to conformational adaptation of the polymer to those bound aggregates which cover more than one A unit. In contrast to other models, the size of a binding site (within the aggregates) is less than one monomeric unit, with n denoting the maximum number of C molecules per A unit in bound aggregates. The model is developed for general n by means of the method of sequence-generating functions. For n = 2 and n = 3, the correctness of the model treatment was checked by the matrix method. The model is applicable to the binding of aggregates to homopolymers, which are flexible enough to fit their structure to the aggregates.     

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

Genome‐scale metabolic models (GEMs) are widely used to calculate metabolic phenotypes. They rely on defining a set of constraints, the most common of which is that the production of metabolites and/or growth are limited by the carbon source uptake rate. However, enzyme abundances and kinetics, which act as limitations on metabolic fluxes, are not taken into account. Here, we present GECKO, a method that enhances a GEM to account for enzymes as part of reactions, thereby ensuring that each metabolic flux does not exceed its maximum capacity, equal to the product of the enzyme's abundance and turnover number. We applied GECKO to a Saccharomyces cerevisiae GEM and demonstrated that the new model could correctly describe phenotypes that the previous model could not, particularly under high enzymatic pressure conditions, such as yeast growing on different carbon sources in excess, coping with stress, or overexpressing a specific pathway. GECKO also allows to directly integrate quantitative proteomics data; by doing so, we significantly reduced flux variability of the model, in over 60% of metabolic reactions. Additionally, the model gives insight into the distribution of enzyme usage between and within metabolic pathways. The developed method and model are expected to increase the use of model‐based design in metabolic engineering.     

A computational algorithm to simulate disorganization of collagen network in injured articular cartilage

Cartilage defects are a known risk factor for osteoarthritis. Estimation of structural changes in these defects could help us to identify high risk defects and thus to identify patients that are susceptible for the onset and progression of osteoarthritis. Here, we present an algorithm combined with computational modeling to simulate the disorganization of collagen fibril network in injured cartilage. Several potential triggers for collagen disorganization were tested in the algorithm following the assumption that disorganization is dependent on the mechanical stimulus of the tissue. We found that tensile tissue stimulus alone was unable to preserve collagen architecture in intact cartilage as collagen network reoriented throughout the cartilage thickness. However, when collagen reorientation was based on both tensile tissue stimulus and tensile collagen fibril strains or stresses, the collagen network architecture was preserved in intact cartilage. Using the same approach, substantial collagen reorientation was predicted locally near the cartilage defect and particularly at the cartilage–bone interface. The developed algorithm was able to predict similar structural findings reported in the literature that are associated with experimentally observed remodeling in articular cartilage. The proposed algorithm, if further validated, could help to predict structural changes in articular cartilage following post-traumatic injury potentially advancing to impaired cartilage function.     

Facilitation promotes invasions in plant‐associated microbial communities

While several studies have established a positive correlation between community diversity and invasion resistance, it is less clear how species interactions within resident communities shape this process. Here, we experimentally tested how antagonistic and facilitative pairwise interactions within resident model microbial communities predict invasion by the plant–pathogenic bacterium Ralstonia solanacearum. We found that facilitative resident community interactions promoted and antagonistic interactions suppressed invasions both in the lab and in the tomato plant rhizosphere. Crucially, pairwise interactions reliably explained observed invasion outcomes also in multispecies communities, and mechanistically, this was linked to direct inhibition of the invader by antagonistic communities (antibiosis), and to a lesser degree by resource competition between members of the resident community and the invader. Together, our findings suggest that the type and strength of pairwise interactions can reliably predict the outcome of invasions in more complex multispecies communities.     

Esterase-type of activity possessed by human plasma apolipoprotein C-II and its synthetic fragments

Human plasma apolipoproteins apoA-I, A-II, C-I, C-II and C-III (with the exception of apoE), porcine pancreatic colipase and procolipase hydrolyze 4-methylumbelliferyloleate. In all cases, liberation of 4-methylumbelliferone could be inhibited by phenylmethylsulfonylfluoride, thus suggesting the involvement of serine residues. To the best of our knowledge this is the first report on the esterase activities of these peptides. Synthetic fragments of the lipoprotein lipase activator, apoC-II, prepared according to the known sequence, also possessed this esterase-type of activity. Furthermore, the esterase-type of activities of the synthetic apoC-II fragments with different chain lengths bore a relatively good correlation to the reported abilities to these peptides to produce activation of lipoprotein lipase.We propose a model for the mechanism of activation of lipoprotein lipase by apolipoprotein C-II. ApoC-II would enhance the apparent catalytic rate constant of lipoprotein lipase by functioning as a specific acyl-enzyme hydrolase. A similar catalytic mechanism is suggested for other protein co-factors of hydrolytic enzymes.     

Fish–duck interactions in boreal lakes in Finland as reflected by abundance correlations

We studied the hypothesis that fish play an important role in lake use by ducks (pairs and broods) in boreal lakes. The study was based on densities of different duck and fish species in 28 boreal lakes in southern Finland. We focused on the three most common duck species (mallard Anas platyrhynchos, green-winged teal A. crecca and common goldeneye Bucephala clangula) and on the three most common fish species (perch Perca fluviatilis, roach Rutilus rutilus and pike Esox lucius) in the region. We considered both competitive and predatory interactions between ducks and fish, the perch and roach being potential competitors with ducks and the pike a potential predator of ducks. We found a negative association between green-winged teal brood density and total fish density, the other duck species having only a weak association with total fish density. When the three fish species were considered separately, a negative association, suggesting food competition, was found between perch, green-winged teal and goldeneye, whereas the role of roach as a food competitor seemed to be of minor importance. We did not find any clear signs of predatory effects of pike on ducks. Our results suggest that food competition is a more important factor than pike predation in affecting lake use by ducks in oligotrophic boreal environments in southern Finland.