Modeling and simulation of Streptomyces peucetius var. caesius N47 cultivation and epsilon-rhodomycinone production with kinetic equations and neural networks

This study focuses on comparing different kinetic growth models and the use of neural networks in the batch cultivation of Streptomyces peucetius var. caesius producing epsilon-rhodomycinone. Contois, Monod and Teissier microbial growth models were used as well as the logistic growth modeling approach, which was found best in the simulations of growth and glucose consumption in the batch growth phase. The lag phase was included in the kinetic model with a CO2 trigger and a delay factor. Substrate consumption and product formation were included as Luedeking-Piret and logistic type equations, respectively. Biomass formation was modeled successfully with a 6-8-2 network, and the network was capable of biomass prediction with an R2-value of 0.983. Epsilon-rhodomycinone production was successfully modeled with a recursive 8-3-1 network capable of epsilon-rhodomycinone prediction with an R2-value of 0.903. The predictive power of the neural networks was superior to the kinetic models, which could not be used in predictive modeling of arbitrary batch cultivations.     

COLONIZATION HISTORY OF THE BALTIC HARBOR SEALS: INTEGRATING ARCHAEOLOGICAL, BEHAVIORAL, AND GENETIC DATA

Detailed knowledge about the history of colonization, population dynamics and behavior greatly enhance evaluation of genetic models of population units and migration rates in spatially structured populations. Here, the genetic uniqueness of harbor seals ( Phoca vitulinia ) in the eastern Baltic is evaluated in the light of new information on the distribution and abundance of Baltic and eastern North Sea populations during the last 11,000 yr, recent hunting statistics, and population counts. Archaeological records reveal that the Baltic population of harbor seals was founded about 8,000 yr ago. Adjacent populations in the North Sea areas were either small, or went extinct, and became significant only during the last 300 yr. This information generates the hypothesis that the Baltic population has been isolated during the last 8,000 yr, despite the lack of geographical barriers. We show that stochastic effects, isolation, and a documented recent population bottleneck can account for the low observed genetic variation in Baltic harbor seals.     

Reproducibility-optimized test statistic for ranking genes in microarray studies

A principal goal of microarray studies is to identify the genes showing differential expression under distinct conditions. In such studies, the selection of an optimal test statistic is a crucial challenge, which depends on the type and amount of data under analysis. While previous studies on simulated or spike-in datasets do not provide practical guidance on how to choose the best method for a given real dataset, we introduce an enhanced reproducibility-optimization procedure, which enables the selection of a suitable gene- anking statistic directly from the data. In comparison with existing ranking methods, the reproducibilityoptimized statistic shows good performance consistently under various simulated conditions and on Affymetrix spike-in dataset. Further, the feasibility of the novel statistic is confirmed in a practical research setting using data from an in-house cDNA microarray study of asthma-related gene expression changes. These results suggest that the procedure facilitates the selection of an appropriate test statistic for a given dataset without relying on a priori assumptions, which may bias the findings and their interpretation. Moreover, the general reproducibilityoptimization procedure is not limited to detecting differential expression only but could be extended to a wide range of other applications as well.     

From plants to birds: higher avian predation rates in trees responding to insect herbivory

BACKGROUND: An understanding of the evolution of potential signals from plants to the predators of their herbivores may provide exciting examples of co-evolution among multiple trophic levels. Understanding the mechanism behind the attraction of predators to plants is crucial to conclusions about co-evolution. For example, insectivorous birds are attracted to herbivore-damaged trees without seeing the herbivores or the defoliated parts, but it is not known whether birds use cues from herbivore-damaged plants with a specific adaptation of plants for this purpose. METHODOLOGY: We examined whether signals from damaged trees attract avian predators in the wild and whether birds could use volatile organic compound (VOC) emissions or net photosynthesis of leaves as cues to detect herbivore-rich trees. We conducted a field experiment with mountain birches (Betula pubescens ssp. czerepanovii), their main herbivore (Epirrita autumnata) and insectivorous birds. Half of the trees had herbivore larvae defoliating trees hidden inside branch bags and half had empty bags as controls. We measured predation rate of birds towards artificial larvae on tree branches, and VOC emissions and net photosynthesis of leaves. PRINCIPAL FINDINGS AND SIGNIFICANCE: The predation rate was higher in the herbivore trees than in the control trees. This confirms that birds use cues from trees to locate insect-rich trees in the wild. The herbivore trees had decreased photosynthesis and elevated emissions of many VOCs, which suggests that birds could use either one, or both, as cues. There was, however, large variation in how the VOC emission correlated with predation rate. Emissions of (E)-DMNT [(E)-4,8-dimethyl-1,3,7-nonatriene], beta-ocimene and linalool were positively correlated with predation rate, while those of highly inducible green leaf volatiles were not. These three VOCs are also involved in the attraction of insect parasitoids and predatory mites to herbivore-damaged plants, which suggests that plants may not have specific adaptations to signal only to birds.     

Effects of temperature and oxygenavailability on greenhouse gas and nutrient dynamics in sediment of a eutrophic mid-boreal lake

The effects of oxygen conditions and temperature on dynamics of greenhousegases (CH₄, CO₂, N₂O) and nutrients(NH₄ ⁺, NO₂ ^–+NO₃ ^–, tot-P) were studied in sediment of hyper-eutrophic LakeKevätön, Finland. Undisturbed sediment cores were incubated at 6, 11,16, and 23 °C in a laboratory microcosm using a continuouswater flowtechnique with an oxic or anoxic water flow. The production of CO₂increased with increasing temperature in both oxic (Q₁₀ 3.2 ±0.6) and anoxic (Q₁₀ 2.3 ± 0.4) flows. The release ofCH₄ increased with temperature in anoxic conditions (Q₁₀2.3 ± 0.2), but was negligible with the oxic flow at all temperatures.The release of NH₄ ⁺ increased with temperature with the oxic and anoxic flows(Q₁₀ 2.4 ± 0.1). There was a net production of NO₂ ^–, NO₃ ^– and N₂O with the oxic flow at temperatures below16 °C. The release of phosphorus was greater from the anoxicsediments and increased with temperature with both the anoxic (Q₁₀2.9 ± 0.5) and oxic (Q₁₀ 1.9 ± 0.1) flows. It isprobable that the temperature of boreal lakes and the associated oxygendeficiency will increase as the climate becomes warmer. Our experiments showedthat this change would increase the global warming potential of greenhousegasesreleased from sediments of eutrophic lakes predominately attributable to theincrease in the CH₄ production. Furthermore, warming would alsoaccelerate the eutrophication of lakes by increasing release of phosphorus andmineral nitrogen from sediments, which further enhance CH₄productionin sediments.     

Crowding-induced responses in a geometrid moth revisited: a field experiment

In Lepidoptera, effects of larval crowding on life history traits may manifest themselves as changes in growth rate and duration of larval period. For the outbreaking geometrid moth, Epirrita autumnata , impacts of crowding have been shown in earlier laboratory studies, and these responses were modified by diet quality. In this study, the aim was to find out the specific nature of crowding effects of E. autumnata in the field. E. autumnata larvae were reared individually and in groups in mesh bags on mountain birch, both on good and poor quality foliage. Three field experiments were carried out with different densities in the crowded treatment (12, 21 and 45 larvae per 100 short shoots of mountain birch), simulating intermediate to severe outbreaks. The study revealed the density interval (12–21) within which impacts of crowding become evident. Significant effects were mostly found with the two highest densities in the crowded treatment combined with poor foliage quality. In those treatments, crowding resulted in 8–12% and 24–33% decrease in pupal mass and larval survival, respectively. The results of the present field experiments, however, did not corroborate the results of earlier laboratory studies: duration of larval period was not substantially affected, net effects of crowding were negative and interactions between crowding and foliage quality were contrary to those obtained in earlier laboratory studies. In many other Lepidoptera as well, the knowledge on responses to crowding may be mostly qualitative since most crowding experiments have been conducted in laboratory.     

Quantitative-Trait-Locus Analysis of Body-Mass Index and of Stature, by Combined Analysis of Genome Scans of Five Finnish Study Groups

In recent years, many genomewide screens have been performed, to identify novel loci predisposing to various complex diseases. Often, only a portion of the collected clinical data from the study subjects is used in the actual analysis of the trait, and much of the phenotypic data is ignored. With proper consent, these data could subsequently be used in studies of common quantitative traits influencing human biology, and such a reanalysis method would be further justified by the nonbiased ascertainment of study individuals. To make our point, we report here a quantitative-trait-locus (QTL) analysis of body-mass index (BMI) and stature (i.e., height), with genotypic data from genome scans of five Finnish study groups. The combined study group was composed of 614 individuals from 247 families. Five study groups were originally ascertained in genetic studies on hypertension, obesity, osteoarthritis, migraine, and familial combined hyperlipidemia. Most of the families are from the Finnish Twin Cohort, which represents a population-wide sample. In each of the five genome scans, approximately 350 evenly spaced markers were genotyped on 22 autosomes. In analyzing the genotype data by a variance-component method, we found, on chromosome 7pter (maximum multipoint LOD score of 2.91), evidence for QTLs affecting stature, and a second locus, with suggestive evidence for linkage to stature, was detected on chromosome 9q (maximum multipoint LOD score of 2.61). Encouragingly, the locus on chromosome 7 is supported by the data reported by Hirschhorn et al. (in this issue), who used a similar method. We found no evidence for QTLs affecting BMI.     

Fungicidal effect of human lactoferrin against Candida albicans

Human lactoferrin (LF) in its iron-free state (apo LF), killed Candida albicans in a time- and dose-dependent way. The lethal effect was stronger at pH 7.0 than at pH 5.5 and maximum inhibition at neutral pH was achieved in 25 min when the fungal cells were exposed to LF in 0.05 mM KCl at 37 degrees C. Fe(3+)-saturated LF had no fungicidal activity. Apo LF-mediated killing was also temperature-dependent with enhanced inhibition at higher temperatures (37 degrees, 42 degrees C). The presence of 1 mM D-glucose did not affect the candidacidal activity of apo LF but both phosphate and bicarbonate ions at physiological salivary concentrations completely blocked the anti-fungal effect. Therefore it seems unlikely that LF belongs to the major host defence factors against oral candidosis.     

A lectin cytochemical study of glycoconjugates in the human retina

Summary The binding to morphologically normal human retina of eleven biotin- or peroxidase-coupled lectins with different carbohydrate specificities was studied. Eight formalin-fixed and paraffin-embedded eyes were examined. Photoreceptor cells bound Lens culinaris (LCA), wheat germ (WGA), peanut (PNA) and Ricinus communis (RCAI) agglutinins, and concanavalin A (ConA). The outer segment region was labeled more strongly than the inner segment region, and PNA labeled only cones. All these lectins except PNA bound to both plexiform layers, and all but PNA and RCAI to the nuclear layers. Pretreatment with neuraminidase to remove sialic acid resulted in increased binding of RCAI and PNA, which now labeled both rods and cones, and in decreased binding of WGA. Bandeiraea simplicifolia (BSAI), Dolichos biflorus (DBA), soybean (SBA), Ulex europaeus (UEAI), and Lotus tetragonolobus (LTA) agglutinins, as well as pokeweed mitogen (PWM) reacted only with retinal vascular endothelial cells, which were also labeled with the other lectins. The results indicate that -mannose, -glucose, -galactose, N-acetyl-d-glucosamine and N-acetylneuraminic acid are present in glycoconjugates of human neuroretina.     

Permeability characteristics and membrane affinity of flavonoids and alkyl gallates in Caco-2 cells and in phospholipid vesicles

Biomembrane interactions of flavonoids and alkyl gallates were investigated using transport studies on Caco-2 cells and membrane affinity experiments in phospholipid vesicles. Flavone was rapidly absorbed across the cell monolayer (P(app),380 x 10(-6) cm/s), whereas efficient uptake but no apical to basolateral transport was observed with the flavonoids with higher degree of hydroxylation (e.g., quercetin and luteolin). The transport of alkyl gallates was governed by the length of the alkyl chain, i.e., methyl and propyl gallate were absorbed while octyl gallate showed cellular uptake but no transport. Flavonoids with several hydroxyl groups exhibited highest affinity for vesicle membranes, partition coefficients being 7.1 and 7.5 microM for luteolin and quercetin, respectively. In conclusion, the degree of hydroxylation, molecular configuration, and length of the side chain of flavonoids and alkyl gallates seem to have a highly important impact on their membrane affinity as well as on their permeability characteristics in Caco-2 cells.