Evaluation of identity-by-descent probabilities for half-sibs on continuous genome

A new method is provided for exact evaluation of the distribution of the amount of genetic material, from a chromosomal segment, shared identical-by-descent by a finite number of half-sibs. The interest in such distribution stems from its relation to the distribution of genetic material from chromosomal segments of an individual surviving to the next generation. The new method is superior to the existing one which has recently been suggested by Stefanov [V.T. Stefanov, Distribution of the amount of genetic material from a chromosomal segment surviving to the following generation. J. Appl. Probab. 41 (2004) 345]. It allows both faster computation and a large number of half-sibs. Relevant software codes are provided for automated implementation of such evaluations.     

Production of 1,3-Propanediol by Clostridium butyricum VPI 3266 in continuous cultures with high yield and productivity

The effects of dilution rate and substrate feed concentration on continuous glycerol fermentation by Clostridium butyricum VPI 3266, a natural 1,3-propanediol producer, were evaluated in this work. A high and constant 1,3-propanediol yield (around 0.65 mol/mol), close to the theoretical value, was obtained irrespective of substrate feed concentration or dilution rate. Improvement of 1,3-propanediol volumetric productivity was achieved by increasing the dilution rate, at a fixed feed substrate concentration of 30, 60 or 70 g l⁻¹. Higher 1,3-propanediol final concentrations and volumetric productivities were also obtained when glycerol feed concentration was increased from 30 to 60 g l⁻¹, at D=0.05–0.3 h⁻¹, and from 60–70 g l⁻¹, at D=0.05 and 0.1 h⁻¹·30 g l⁻¹ of 1,3-propanediol and the highest reported value of productivity, 10.3 g l⁻¹ h⁻¹, was achieved at D=0.30 h⁻¹ and 60 g l⁻¹ of feed glycerol. A switch to an acetate/butyrate ratio higher than one was observed for 60 g l⁻¹ of feed glycerol and a dilution rate higher than 0.10 h⁻¹; moreover, at D=0.30 h⁻¹ 3-hydroxypropionaldehyde accumulation was observed for the first time in the fermentation broth of C. butyricum.     

Elucidation of T cell signalling models

A potential mechanism that allows T cells to reliably discriminate pMHC ligands involves an interplay between kinetic proofreading, negative feedback and a destruction of this negative feedback. We analyse a detailed model of these mechanisms which involves the TCR, SHP1 and ERK. We discover that the behaviour of pSHP1 negative feedback is of primary importance, and particularly the influence of a kinetic proofreading base negative feedback state on pSHP1 dynamics. The CD8 co-receptor is shown to benefit from a kinetic proofreading locking mechanism and is able to overcome pSHP1 negative influences to sensitise a T cell.     

How icosahedral are icosahedral clusters?

Icosahedral symmetry, not contemplated within the crystallographic space groups, is nevertheless present to a high degree of perfection in a variety of clusters, in molecular, ionic, covalent or metallic structures. The application of continuous shape measures to those structures allows for a quantification of the degree of icosahedral symmetry present in each case, a first necessary step for a deeper discussion of the factors that favor the adoption of the icosahedron as a stable structural motif. Examples analyzed include boranes and carbaboranes, main group, rare earth or transition metal clusters, ligand-bridged polynuclear complexes and sets of donor atoms in mono- or polynuclear complexes. Specific examples are found of structures that appear along the minimal distortion pathways from the icosahedron to the cuboctahedron or the anticuboctahedron.     

Effects of glutamate on microbial efficiency and metabolism in continuous culture of ruminal contents and on performance of mid-lactation dairy cows

Three experiments were conducted to determine (1) the dose of glutamate needed to alter fermentation and nitrogen (N) partitioning in a continuous culture system, (2) the effect of supplemental glutamate in diets varying in rumen-undegradable protein on fermentation and N partitioning in a continuous culture system, and (3) the effect of dietary supplemental glutamate on the lactational performance of mid-lactation dairy cows, total tract nutrient digestibility, and ruminal microbial N synthesis. In experiment 1, the equivalent of 0, 40, or 80 g of supplemental glutamate per cow per day was added to a basal diet. The dietary treatments were evaluated in a continuous culture system. Glutamate decreased protein digestion and microbial growth while increasing non-ammonia, non-microbial N. Within the doses tested, the equivalent of 80 g glutamate per cow per day most effectively increased non-ammonia, non-microbial N. In experiment 2, dietary treatments consisted of diets formulated to have low rumen-undegradable protein (LRUP; 62 g/kg DM), low rumen-undegradable protein plus the equivalent of 80 g glutamate per cow per day (LRUP + G), and high rumen-undegradable protein [HRUP; 68 g/kg dry matter (DM)]. The dietary treatments were evaluated in a continuous culture system. When added to a diet low in rumen-undegradable protein, glutamate tended to decrease DM and organic matter (OM) digestibility, decreased total volatile fatty acid (VFA) production, increased fermenter pH, increased feed N converted to microbial N, and had no effect on microbial N production. The LRUP + G diet was similar to the HRUP diet and different from the LRUP diet in feed N converted to microbial N and ammonia N concentration. In experiment 3, 40 Holstein cows were utilized in a crossover study to test the effects of two dietary treatments: 0 or 80 g of supplemental glutamate per cow per day. The addition of glutamate to the diet of lactating dairy cows did not improve lactational performance or nutrient digestibility. Based on the results from these in vitro and in vivo experiments, the addition of glutamate to lactating cow diets is not recommended.     

Continuous immobilized yeast reactor system for complete beer fermentation using spent grains and corncobs as carrier materials

Despite extensive research carried out in the last few decades, continuous beer fermentation has not yet managed to outperform the traditional batch technology. An industrial breakthrough in favour of continuous brewing using immobilized yeast could be expected only on achievement of the following process characteristics: simple design, low investment costs, flexible operation, effective process control and good product quality. The application of cheap carrier materials of by-product origin could significantly lower the investment costs of continuous fermentation systems. This work deals with a complete continuous beer fermentation system consisting of a main fermentation reactor (gas-lift) and a maturation reactor (packed-bed) containing yeast immobilized on spent grains and corncobs, respectively. The suitability of cheap carrier materials for long-term continuous brewing was proved. It was found that by fine tuning of process parameters (residence time, aeration) it was possible to adjust the flavour profile of the final product. Consumers considered the continuously fermented beer to be of a regular quality. Analytical and sensorial profiles of both continuously and batch fermented beers were compared.     

Metabolism of lactose by Clostridium thermolacticum growing in continuous culture

The objective of the present study was to characterize the metabolism of Clostridium thermolacticum, a thermophilic anaerobic bacterium, growing continuously on lactose (10 g l⁻¹) and to determine the enzymes involved in the pathways leading to the formation of the fermentation products. Biomass and metabolites concentration were measured at steady-state for different dilution rates, from 0.013 to 0.19 h⁻¹. Acetate, ethanol, hydrogen and carbon dioxide were produced at all dilution rates, whereas lactate was detected only for dilution rates below 0.06 h⁻¹. The presence of several key enzymes involved in lactose metabolism, including beta-galactosidase, glyceraldehyde-3-phosphate dehydrogenase, pyruvate:ferredoxin oxidoreductase, acetate kinase, ethanol dehydrogenase and lactate dehydrogenase, was demonstrated. Finally, the intracellular level of NADH, NAD⁺, ATP and ADP was also measured for different dilution rates. The production of ethanol and lactate appeared to be linked with the re-oxidation of NADH produced during glycolysis, whereas hydrogen produced should come from reduced ferredoxin generated during pyruvate decarboxylation. To produce more hydrogen or more acetate from lactose, it thus appears that an efficient H₂ removal system should be used, based on a physical (membrane) or a biological approach, respectively, by cultivating C. thermolacticum with efficient H₂ scavenging and acetate producing microorganisms.     

Purification and characterization of hydrosoluble components from the sap of Chinese lacquer tree Rhus vernicifera

Continuous gradient elution chromatography (CGEC) was employed to purify and separate enzymes and polysaccharides from the sap of Rhus vernicifera Chinese lacquer tree. There are three different molecules with laccase enzyme activity. Two are enzymes of each other (L1, and L2), whereas the third (RL) is an entirely separate entity. Two polysaccharides (GP1 and GP2) were also found. The Rhus laccase (RL), and isoenzymes L1 and L2, have peak molecular masses of 109,100, 120,000, 103,000 respectively; each has four copper atoms per molecule, and the pI values were 8.2, 8.6, and 9.1, respectively. The structure of the laccases was studied by Fourier-transform infrared (FT-IR) and Matrix-assisted laser desorption/ionization time-of flight (MALDI-TOF) mass spectrometry. The typical amide I (1646 cm⁻¹) and amide II (1545 cm⁻¹) bands were observed. The results from MALDI-TOF were similar to those from CGEC, but the molecular mass from the MALDI-TOF was significantly different from that obtained from sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE).     

Self-Organizing Maps in Revealing Variation in Non-obligatory Riverine Fish in Long-term Data

Sensitiveness to the overall influence of the river channel regulation, impoundment and pollution was studied for 12 non-obligatory riverine (NOR) fish species in the Warta River, Poland, over the period of 1963–1998. Their total abundance has not considerably changed unlike the structure of their aggregation, which was revealed by a self-organizing map (SOM, Kohonen unsupervised artificial neural network) almost perfectly separating 1960s samples from 1990s ones. The greatest changes in proportion were recorded for the dominant roach Rutilus rutilus (from 28.6 to 60.0%), perch Perca fluviatilis (1.9 to 9.5%), pike Esox lucius (2.9 to 4.9%), and the former codominant bleak Alburbus alburnus (22.9 to 1.8%). They resulted from highly significant (p < 0.001), reaching even one order of magnitude, differences in the abundance of these species. Such remarkable alternations in dominant NOR ichthyofauna obviously influenced the whole fish assemblage structure, which was best illustrated by a clear vertical gradient over SOM in Simpson and Shannon indices. Thus, NOR species, both studied together and separately, can supply valuable information on the fish assemblage dynamics and should not be neglected in temporal analyses, often focused only on vulnerable obligatory riverine, migratory and/or endemic species.     

How is the equilibrium of continuous strategy game different from that of discrete strategy game?

Cooperation in the prisoner's dilemma (PD) played on various networks has been explained by so-called network reciprocity. Most of the previous studies presumed that players can offer either cooperation (C) or defection (D). This discrete strategy seems unrealistic in the real world, since actual provisions might not be discrete, but rather continuous. This paper studies the differences between continuous and discrete strategies in two aspects under the condition that the payoff function of the former is a linear interpolation of the payoff matrix of the latter. The first part of this paper proves theoretically that for two-player games, continuous and discrete strategies have different equilibria and game dynamics in a well-mixed but finite population. The second part, conducting a series of numerical experiments, reveals that such differences become considerably large in the case of PD games on networks. Furthermore, it shows, using the Wilcoxon sign-rank test, that continuous and discrete strategy games are statistically significantly different in terms of equilibria. Intensive discussion by comparing these two kinds of games elucidates that describing a strategy as a real number blunts D strategy invasion to C clusters on a network in the early stage of evolution. Thus, network reciprocity is enhanced by the continuous strategy.