Comparison of arbitrarily primed polymerase chain reaction and ribotyping for subtyping Actinobacillus actinomycetemcomitans

This study investigated the compatibility of arbitrarily primed polymerase chain reaction (AP-PCR) and ribotyping in the characterization of Actinobacillus actinomycetemcomitans , a major pathogen in the mixed anaerobic microflora of human periodontitis. AP-PCR was performed directly on lysed bacterial colonies using a random-sequence 10-base oligonucleotide primer. Ribotyping was carried out by using purified bacterial chromosomal DNA digested with BglI. DNA fragments were separated electrophoretically, blotted onto a nylon membrane and hybridized with the plasmid pKK3535 containing the rRNA operon of Escherichia coli. The two genetic methods were evaluated on isolates from single individuals and from family members. Twelve AP-PCR types and 47 ribotypes were distinguished among 76 A. actinomycetemcomitans isolates of different serotypes. AP-PCR typing and ribotyping gave compatible results in 18 of 20 comparisons. Although AP-PCR detected less genetic heterogeneity in A. actinomycetemcomitans than ribotyping, the rapid and relatively simple AP-PCR technique seems to be sufficiently discriminative to be used in large scale epidemiological studies which preclude the application of the more laborious ribotyping technique.     

Continuous representations of time-series gene expression data.

We present algorithms for time-series gene expression analysis that permit the principled estimation of unobserved time points, clustering, and dataset alignment. Each expression profile is modeled as a cubic spline (piecewise polynomial) that is estimated from the observed data and every time point influences the overall smooth expression curve. We constrain the spline coefficients of genes in the same class to have similar expression patterns, while also allowing for gene specific parameters. We show that unobserved time points can be reconstructed using our method with 10-15% less error when compared to previous best methods. Our clustering algorithm operates directly on the continuous representations of gene expression profiles, and we demonstrate that this is particularly effective when applied to nonuniformly sampled data. Our continuous alignment algorithm also avoids difficulties encountered by discrete approaches. In particular, our method allows for control of the number of degrees of freedom of the warp through the specification of parameterized functions, which helps to avoid overfitting. We demonstrate that our algorithm produces stable low-error alignments on real expression data and further show a specific application to yeast knock-out data that produces biologically meaningful results.     

Overwintering and migration behaviour of post-spawned Atlantic salmon Salmo salar in a large hydropower-regulated river and reservoir

Tracking 47 post-spawned adult Atlantic salmon Salmo salar L. in a hydropower-regulated river through autumn, winter and spring revealed that winter survival was 56% and 75% in two study years, respectively, with higher mortality of males than females (50% vs. 33% and 100% vs. 13%, respectively). Some kelts (n = 7) displayed nondirected movements that were interpreted as a reconditioning period for an average of 9–17 days prior to directed downstream movements indicating the initiation of migration. Survival after the initiation of migration in spring was 83% and 94% to the hydropower dam in the first and second study years, and decreased to 60 and 63%, respectively, after dam passage. There were no further losses in the downriver reach in the second year, with the first year having a cumulative survival estimate of 53% to the river mouth. Kelts approached the dam when the spillway gates were available as a passage option most of the time (64%–75%), but some kelts arrived at the dam or had not yet passed when spillways were closed (n = 6) and the only remaining passage option was restricted to the turbines. However, all but one kelt that must have passed via turbine were successful in reaching the river mouth. Migratory delay presumably due to searching behaviour caused by low water flow was estimated at approximately 6 days as migration rates were significantly slower in the reservoir (median ± s.e. 8.5 ± 2.5 km day⁻¹) than up- (29.7 ± 5.0 km day⁻¹) or downriver (22.1 ± 3.1 km day⁻¹). The proportion of time (median 30%) that kelts spent swimming upstream (searching behaviour) in the reservoir was a significant variable for migration success.     

Structural Basis for Complement Evasion by Lyme Disease Pathogen Borrelia burgdorferi

Borrelia burgdorferi spirochetes that cause Lyme borreliosis survive for a long time in human serum because they successfully evade the complement system, an important arm of innate immunity. The outer surface protein E (OspE) of B. burgdorferi is needed for this because it recruits complement regulator factor H (FH) onto the bacterial surface to evade complement-mediated cell lysis. To understand this process at the molecular level, we used a structural approach. First, we solved the solution structure of OspE by NMR, revealing a fold that has not been seen before in proteins involved in complement regulation. Next, we solved the x-ray structure of the complex between OspE and the FH C-terminal domains 19 and 20 (FH19-20) at 2.83 Å resolution. The structure shows that OspE binds FH19-20 in a way similar to, but not identical with, that used by endothelial cells to bind FH via glycosaminoglycans. The observed interaction of OspE with FH19-20 allows the full function of FH in down-regulation of complement activation on the bacteria. This reveals the molecular basis for how B. burgdorferi evades innate immunity and suggests how OspE could be used as a potential vaccine antigen.     

Net climate impacts of forest biomass production and utilization in managed boreal forests

In this work, we studied the potentials offered by managed boreal forests and forestry to mitigate the climate change using forest‐based materials and energy in substituting fossil‐based materials (concrete and plastic) and energy (coal and oil). For this purpose, we calculated the net climate impacts (radiative forcing) of forest biomass production and utilization in the managed Finnish boreal forests (60°–70°N) over a 90‐year period based on integrated use forest ecosystem model simulations (on carbon sequestration and biomass production of forests) and life‐cycle assessment (LCA) tool. When studying the effects of management on the radiative forcing in a system integrating the carbon sink/sources dynamics in both biosystem and technosystem, the current forest management (baseline management) was used a reference management. Our results showed that the use of forest‐based materials and energy in substituting fossil‐based materials and energy would provide an effective option for mitigating climate change. The negative climate impacts could be further decreased by maintaining forest stocking higher over the rotation compared to the baseline management and by harvesting stumps and coarse roots in addition to logging residues in the final felling. However, the climate impacts varied substantially over time depending on the prevailing forest structure and biomass assortment (timber, energy biomass) used in substitution.     

Food‐web structure and mercury dynamics in a large subarctic lake following multiple species introductions

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Exogenous melatonin affects lipids and enzyme activities in mink (Mustela vison) liver

Exogenous melatonin as subcutaneous 2.7-mg implants was given to eight female and male minks in late July with an equal number of animals in the control groups. The liver enzyme activities and major lipids of liver and plasma were measured in October-November. Melatonin had very pronounced effects on the lipid and carbohydrate metabolism of the minks and there was also a clear sexual dimorphism. In the males, melatonin decreased the lipase esterase activity of the liver. In the liver of the females, however, melatonin increased the glucose-6-phosphatase activity. Due to melatonin treatment the liver triacylglycerol contents diminished in both sexes. At the same time, in the females the liver cholesterol levels were decreased. In the plasma lipids, the only change was a fall in the polar lipids of the melatonin-treated females. Melatonin seems to be responsible for the metabolic changes associated with the onset of wintering, especially for the acceleration of the deposition of subcutaneous fat reserves. The smaller females experience the effects of exogenous melatonin more rapidly than the males. Perhaps the smaller body size requires an earlier onset of metabolic preparation for the winter.     

Seasonal weight regulation of the raccoon dog (Nyctereutes procyonoides): interactions between melatonin,leptin, ghrelin,and growth hormone

The raccoon dog (Nyctereutes procyonoides, Canidae, Carnivora) is a middle-sized omnivore with excessive autumnal fattening and winter sleep. We studied seasonal weight regulation of the species by following the plasma leptin, ghrelin, and growth hormone (GH) levels of farm-bred raccoon dogs (n = 32) for 6 months. In August, half of the raccoon dogs received continuous-release melatonin implants, and in November, half of the animals of both the sham-operated and melatonin-treated groups were fasted for 2 months. In the autumn, the plasma leptin and GH levels were low, but the ghrelin levels were relatively high and correlated positively with energy intake. This represents the period of energy storage. Leptin and GH levels peaked simultaneously in late October, and melatonin advanced the peaks by 1 week. Thereafter, the levels rapidly declined, representing the transition period from autumnal anabolism to wintertime catabolism. In the winter, the leptin and GH levels rose to high levels, but the ghrelin-leptin ratio was very low. This is the period of winter sleep, with fat accumulated in the autumn as the principal metabolic fuel. In the winter, leptin, ghrelin, and GH may work in synergy to increase lipolysis. GH may also induce winter sleep to the raccoon dog. Fasting had no effect on the hormone levels, unlike in humans and rodents. Instead of the amount of fat in the body, the main regulators of the levels of these hormones in the raccoon dog are presumably seasonal rhythms entrained by melatonin.     

Seasonal reproductive endocrine profile of the raccoon dog (Nyctereutes procyonoides)-effects of melatonin and food deprivation

The raccoon dog (Nyctereutes procyonoides, Canidae, Carnivora) is a middle-sized omnivore with excessive autumnal fattening and winter sleep. We studied adaptations of the species to boreal climate and photoperiod by following the plasma reproductive and thyroid hormone concentrations of farm-bred raccoon dogs (n=32) for 12 months. On August 16, 2000, and February 8, 2001, half of the raccoon dogs received continuous-release melatonin implants (the MEL group). The other half was sham-operated (the SHAM group). Between November 27, 2000, and January 25, 2001, half of the animals of both groups were fasted. The plasma testosterone concentrations of the MEL males peaked in February, a month earlier than in the SHAM males. Autumnal melatonin treatment also advanced the gestation period reflected by the plasma progesterone concentrations by seven weeks. Food deprivation in winter seems to accentuate the sex steroid response during the mating as the fasted males had higher testosterone concentrations than the fed males in February and March.