Flexible life history responses to flower and rosette bud removal in three perennial herbs

In a garden experiment we investigated the response to continuous removal of either flower buds or rosette buds in three perennial grassland species ( Hypochaeris radicata , Succisa pratensis and Centaurea jacea ), which differ in longevity and flowering type. We distinguished two possible responses: compensation for lost buds by making more buds of the same type, and switching towards development of other life history functions. Both responses were demonstrated in our experiment, but bud removal had significantly different effects in each of the three species. The degree of compensation and the expression of trade-offs between life history functions differed markedly between species and seem related to longevity and developmental constraints. With respect to switching, our results suggest costs of reproduction and a trade-off between life history functions, at least for Hypochaeris and Succisa . For these species weight of new rosettes increased when resource allocation to flowering was inhibited. In Hypochaeris, we see that both compensation for lost flower buds and switching from lost rosette buds increased production of flower buds, underscoring the pivotal role of sexual reproduction in this short-lived species. The most prominent response seen in Centaurea is compensation for lost rosette buds, indicating that this long-lived species with monocarpic rosettes relies on rosette formation. Although Succisa does respond to bud removal, time is an important constraint in this species with long-lived rosettes and preformed flowering stalks. Trade-offs in Succisa seem to operate at a larger time scale, requiring long-lasting experiments to reveal them. We conclude that the response of these species to inflicted damage is likely to be linked to their longevity and developmental constraints.     

Effects of Dietary Non-Digestible Oligosaccharides on Microbial Characteristics of Ileal Chyme and Faeces in Weaner Pigs

Fructooligosaccharides (FOS) and transgalactooligosaccharides (TOS), which are non-digestible oligosaccharides (NDO), were included at 10 and 40g/kg in an NDO-free control diet at the expense of purified cellulose. Each of the 5 diets was fed to 4 weaner pigs and microbial characteristics of their ileal chyme and faeces were assessed. The NDO-pigs had lower ileal pH than the control pigs. Dietary NDO did not affect the ileal volatile fatty acid concentration, though FOS-pigs had a higher concentration of lactic acid and relatively more iso-valeric acid and less acetic acid than TOS-pigs. The NDO-pigs had lower ileal aerobic bacterial counts than the control pigs, whilst the FOS-pigs had a larger ileal anaerobic bacterial counts than the TOS-pigs. The NDO-pigs had an higher faecal pH and their faecal volatile fatty acid pool contained relatively more iso-butyric acid and iso-valeric acid than the control pigs. The TOS-pigs tended to have higher faecal anaerobic bacterial counts and had a smaller concentration of faecal volatile fatty acid than the FOS-pigs. We concluded that whilst effects at the faecal level may have been partly due to a reduced intake of cellulose, dietary NDO can exert precaecal prebiotic effects in weaner pigs.     

Transglycosidase activity of Bifidobacterium adolescentis DSM 20083 α-galactosidase

Bifidobacterium adolescentis, a gram-positive saccharolytic bacterium found in the human colon, can, alongside other bacteria, utilise stachyose in vitro thanks to the production of an α-galactosidase. The enzyme was purified from the cell-free extract of Bi. adolescentis DSM 20083^T. It was found to act with retention of configuration (α→α), releasing α-galactose from p-nitrophenyl galactoside. This hydrolysis probably operates with a double-displacement mechanism, and is consistent with the observed glycosyltransferase activity. As α-galactosides are interesting substrates for bifidobacteria, we focused on the production of new types of α-galactosides using the transgalactosylation activity of Bi. adolescentisα-galactosides. Starting from melibiose, raffinose and stachyose oligosaccharides could be formed. The transferase activity was highest at pH 7 and 40 °C. Starting from 300 mM melibiose a maximum yield of 33% oligosaccharides was obtained. The oligosaccharides formed from melibiose were purified by size-exclusion chromatography and their structure was elucidated by NMR spectroscopy in combination with enzymatic degradation and sugar linkage analysis. The trisaccharide α-d-Galp-(1 → 6)-α-d-Galp-(1 → 6)-d-Glcp and tetrasaccharide α-d-Galp-(1 → 6)-α-d-Galp-(1 → 6)-α-d-Galp-(1 → 6)-d-Glcp were identified, and this indicates that the transgalactosylation to melibiose occurred selectively at the C-6 hydroxyl group of the galactosyl residue. The trisaccaride α-d-Galp-(1 → 6)-α-d-Galp-(1 → 6)-d-Glcp formed could be utilised by various intestinal bacteria, including various bifidobacteria, and might be an interesting pre- and synbiotic substrate. Received: 15 March 1999 / Received revision: 8 June 1999 / Accepted: 11 June 1999     

Automated constraint-based nucleotide sequence selection for DNA computation

We present techniques for automating the design of computational systems built using DNA, given a set of high-level constraints on the desired behavior and performance of the system. We have developed a program called SCAN that exploits a previously implemented computational melting temperature primitive to search a 'nucleotide space' for sequences satisfying a pre-specified set of constraints, including hybridization discrimination, primer 5' end and 3' end stability, secondary structure reduction, and prevention of oligonucleotide dimer formation. The first version of SCAN utilized 24 h of computer time to search a space of over 7.5 billion unary counter designs and found only nine designs satisfying all of the pre-specified constraints. One of SCAN's designs has been implemented in the laboratory and has shown a marked improvement in performance over the products of previous attempts at manual design. We conclude with some novel ideas for improving the overall speed of the program that offer the promise of an efficient method for selecting optimal nucleotide sequences in an automated fashion.     

Theoretical and practical advances in genome halving

MOTIVATION: Duplication of an organism's entire genome is a rare but spectacular event, enabling the rapid emergence of multiple new gene functions. Over time, the parallel linkage of duplicated genes across chromosomes may be disrupted by reciprocal translocations, while the intra-chromosomal order of genes may be shuffled by inversions and transpositions. Some duplicate genes may evolve unrecognizably or be deleted. As a consequence, the only detectable signature of an ancient duplication event in a modern genome may be the presence of various chromosomal segments containing parallel paralogous genes, with each segment appearing exactly twice in the genome. The problem of reconstructing the linkage structure of an ancestral genome before duplication is known as genome halving with unordered chromosomes. RESULTS: In this paper, we derive a new upper bound on the genome halving distance that is tighter than the best known, and a new lower bound that is almost always tighter than the best known. We also define the notion of genome halving diameter, and obtain both upper and lower bounds for it. Our tighter bounds on genome halving distance yield a new algorithm for reconstructing an ancestral duplicated genome. We create a software package GenomeHalving based on this new algorithm and test it on the yeast genome, identifying a sequence of translocations for halving the yeast genome that is shorter than previously conjectured possible.     

Survival of Lactobacillus plantarum 44a after spraying and drying in feed and during exposure to gastrointestinal tract fluids in vitro

A good probiotic strain should be able to survive the conditions of handling and storage to be delivered in high concentration to the host. That is especially important when stressful conditions are prevalent in the carrier, for instance in low water content foods like animal feed. The aim of this research was to study the survival of the probiotic candidate Lactobacillus plantarum 44a after spraying and drying in feed, and during storage and exposure to gastrointestinal tract fluids in vitro. In addition, the viability of the strain during exposure to distilled water and 2% NaCl was studied. Feed was sprayed with a suspension of asymptotically equal to 2 x 10(10) CFU of L. plantarum 44a in 10, 15, 20, 25 and 30% v/w of the feed and dried to constant weight (6% moisture) in a convective oven at 25 degrees C. L. plantarum 44a survived 14.67, 36, 51.86, 78.9 and 105.3% respectively in relation to the original % v/w of the feed. After 3 weeks of storage at 25 degrees C, survival was similarly low in all the treatments. L. plantarum 44a stored in feed containing 13% moisture, vacuum-packaged and stored in refrigeration, maintained high viability (approximately 100%) after 1 year of storage. Survival was not affected after feed-containing lactobacilli was exposed to gastrointestinal fluids in a simulation model. Viability of L. plantarum 44a as a cell suspension in PBS added directly to distilled water or distilled water with 2% NaCl was maintained up to 48 h; after 72 h, viability started to decline. It is concluded that L. plantarum 44a maintained high viability after being dried and stored in feed even after exposure to gastric and intestinal fluids in vitro.     

Digital Mapping of Soil Organic Carbon Contents and Stocks in Denmark

Estimation of carbon contents and stocks are important for carbon sequestration, greenhouse gas emissions and national carbon balance inventories. For Denmark, we modeled the vertical distribution of soil organic carbon (SOC) and bulk density, and mapped its spatial distribution at five standard soil depth intervals (0−5, 5−15, 15−30, 30−60 and 60−100 cm) using 18 environmental variables as predictors. SOC distribution was influenced by precipitation, land use, soil type, wetland, elevation, wetness index, and multi-resolution index of valley bottom flatness. The highest average SOC content of 20 g kg⁻¹ was reported for 0−5 cm soil, whereas there was on average 2.2 g SOC kg⁻¹ at 60−100 cm depth. For SOC and bulk density prediction precision decreased with soil depth, and a standard error of 2.8 g kg⁻¹ was found at 60−100 cm soil depth. Average SOC stock for 0−30 cm was 72 t ha⁻¹ and in the top 1 m there was 120 t SOC ha⁻¹. In total, the soils stored approximately 570 Tg C within the top 1 m. The soils under agriculture had the highest amount of carbon (444 Tg) followed by forest and semi-natural vegetation that contributed 11% of the total SOC stock. More than 60% of the total SOC stock was present in Podzols and Luvisols. Compared to previous estimates, our approach is more reliable as we adopted a robust quantification technique and mapped the spatial distribution of SOC stock and prediction uncertainty. The estimation was validated using common statistical indices and the data and high-resolution maps could be used for future soil carbon assessment and inventories.