Optimization of a Bifidobacterium longum production process

Bifidobacteria are used as probiotics mainly in the dairy industry as cell suspensions or as freeze-dried additives. So far there have been no reports on a thorough investigation on factors influencing the production process or a statistical approach to the optimization thereof. A 2(8-4) fractional factorial design was used in determining the critical parameters influencing bioreactor cultivations of Bifidobacterium longum ATCC 15707. Glucose, yeast extract and l-cysteine concentrations were found critical for the cultivation of this strain. Glucose and yeast extract concentrations were further studied together with temperature in a three factor central composite design. The optimized cultivation conditions were temperature 40 degrees C, yeast extract concentration 35 gl(-1) and glucose concentration 20 gl(-1). Freeze-drying of frozen cell suspensions of B. longum was studied first in controlled temperatures and thereafter with temperature programming experiments. The results were statistically evaluated. A temperature program with a 2 h temperature gradient from -10 to 0 degrees C, a 10 h temperature gradient from 0 to +10 degrees C and a 12 h temperature hold at +10 degrees C was found best for the freeze-drying process. Temperature programming reduced drying times by over 50% and improved the product activity by over 160%.     

Predator-induced synchrony in population oscillations of coexisting small mammal species

Comprehensive analyses of long-term (1977-2003) small-mammal abundance data from western Finland showed that populations of Microtus voles (field voles M. agrestis and sibling voles M. rossiaemeridionalis) voles, bank (Clethrionomys glareolus) and common shrews (Sorex araneus) fluctuated synchronously in 3 year population cycles. Time-series analyses indicated that interspecific synchrony is influenced strongly by density-dependent processes. Synchrony among Microtus and bank voles appeared additionally to be influenced by density-independent processes. To test whether interspecific synchronization through density-dependent processes is caused by predation, we experimentally reduced the densities of the main predators of small mammals in four large agricultural areas, and compared small mammal abundances in these to those in four control areas (2.5-3 km(2)) through a 3 year small-mammal population cycle. Predator reduction increased densities of the main prey species, Microtus voles, in all phases of the population cycle, while bank voles, the most important alternative prey of predators, responded positively only in the low and the increase phase. Manipulation also increased the autumn densities of water voles (Arvicola terrestris) in the increase phase of the cycle. No treatment effects were detected for common shrews or mice. Our results are in accordance with the alternative prey hypothesis, by which predators successively reduce the densities of both main and alternative prey species after the peak phase of small-mammal population cycles, thus inducing a synchronous low phase.     

Birds help plants: a meta-analysis of top-down trophic cascades caused by avian predators

The tritrophic interactions between plants, herbivores and avian predators are complex and prone to trophic cascades. We conducted a meta-analysis of original articles that have studied birds as predators of invertebrate herbivores, to compare top-down trophic cascades with different plant responses from different environments and climatic areas. Our search found 29 suitable articles, with a total of 81 separate experimental study set-ups. The meta-analysis revealed that plants benefited from the presence of birds. A significant reduction was observed in the level of leaf damage and plant mortality. The presence of birds also positively affected the amount of plant biomass, whereas effects on plant growth were negligible. There were no differences in the effects between agricultural and natural environments. Similarly, plants performed better in all climatic areas (tropical, temperate and boreal) when birds were present. Moreover, both mature plants and saplings gained benefits from the presence of birds. Our results show that birds cause top-down trophic cascades and thus they play an integral role in ecosystems.     

Does application of methyl jasmonate to birch mimic herbivory and attract insectivorous birds in nature?

Earlier studies have suggested that insectivorous birds, similar to invertebrate predators and parasitoids, may be guided by herbivore-induced plant volatiles (HIPVs) to damaged, herbivore-rich trees. Recent studies have also shown that birds use olfaction more than previously thought, underlying the potential for HIPVs to be sensed by insectivorous birds and utilised during foraging for prey. The HIPV production in plants is mediated, at least partly, by the jasmonic acid signalling pathway, and similar HIPVs to those induced by herbivores can often be induced by exposing plants to methyl jasmonate (MeJa). We studied the effects of MeJa on volatile emission and bird attraction using mature mountain birches (Betula pubescens ssp. czerepanovii) under natural conditions in northern Finland. Experimental trees were assigned to four treatment groups: herbivore-damaged [autumnal moth (Epirrita autumnata)], higher dose of MeJa (30 mM), lower dose of MeJa (15 mM) and control. All trees had three branches covered with mesh bags, but there were larvae inside the bags only of the herbivore-damage treatment. Bird predation rate was monitored with artificial plasticine larvae which were checked daily for peck marks. Birds most often pecked the larvae in the herbivore-damaged trees, but the attractiveness of MeJa-treated trees did not differ from the control. High within-treatment variation in systemic HIPV emissions probably masked MeJa treatment effects. The bird predation rate was high in birches that emitted large amounts of α-pinene. Thus, α-pinene may be one cue used by birds to find herbivore-rich birches.     

Increasing vole numbers cause more lethal damage to saplings in tree monocultures than in mixed stands

Overall, mammalian herbivores are more harmful in mixed plantations than in monocultures, but the effect of herbivore abundance has not been experimentally tested in this context. It has been proposed that there is a critical threshold density where herbivore pressure spreads from preferred plants to everything edible, leading to non-linear density effects on low-quality plants. We experimentally investigated whether survival of an unpalatable plant is similarly related to herbivore density in both monocultures and mixed stands. This we did by establishing monocultures of unpalatable black alder (Alnus glutinosa) and mixed stands of black alder and five more palatable tree species in enclosures, where Microtus voles were introduced and their abundances monitored.The effect of stand diversity tended to depend on vole abundance. Vole damage of tree saplings did not differ between monocultures and mixed stands, but at higher vole abundances attacks had a stronger effect on sapling survival in the monocultures. Sapling survival showed a significant drop in the monocultures at peak abundance of approximately 300 voles ha^?1. In monocultures herbivores do not have alternatives and therefore are forced to become deadlier consumers.     

Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays

Probe defects are a major source of noise in gene expression studies. While existing approaches detect noisy probes based on external information such as genomic alignments, we introduce and validate a targeted probabilistic method for analyzing probe reliability directly from expression data and independently of the noise source. This provides insights into the various sources of probe-level noise and gives tools to guide probe design.     

The effect of temperature and pH gradients on Lactobacillus rhamnosus gene expression of stress-related genes

In this study, Lactobacillus rhamnosus, a renowned probiotic, was cultivated in fluctuating environment. Base gradients caused by a pH control in an industrial process and temperature gradients caused by uneven heating were simulated with a scale-down method. A pH gradient was created in a plug flow reactor (PFR). Expression of pH stress-related genes (atpA, aldB, cfa, groEL, hrcA and pstS) were studied as a relative gene expression study using ldhD as a reference gene. Expression measurements were carried out with the TRAC method. The responses of groEL, hrcA and atpA genes to temperature and pH changes were observed. The expression of phosphate uptake system-related pstS gene was induced almost linearly in the chemostat cultivation experiments when the base gradient in the PFR was increased. Correlations between the results from gene expression studies and freeze stability or acid stress survival were studied. However, by measuring the expression of these genes, we were not able to predict eventual freeze stability or survival from the acid stress test.     

Novel susceptibility locus at 22q11 for diabetic nephropathy in type 1 diabetes

Background

Diabetic nephropathy (DN) affects about 30% of patients with type 1 diabetes (T1D) and contributes to serious morbidity and mortality. So far only the 3q21–q25 region has repeatedly been indicated as a susceptibility region for DN. The aim of this study was to search for new DN susceptibility loci in Finnish, Danish and French T1D families.

Methods and Results

We performed a genome-wide linkage study using 384 microsatellite markers. A total of 175 T1D families were studied, of which 94 originated from Finland, 46 from Denmark and 35 from France. The whole sample set consisted of 556 individuals including 42 sib-pairs concordant and 84 sib-pairs discordant for DN. Two-point and multi-point non-parametric linkage analyses were performed using the Analyze package and the MERLIN software. A novel DN locus on 22q11 was identified in the joint analysis of the Finnish, Danish and French families by genome-wide multipoint non-parametric linkage analysis using the Kong and Cox linear model (NPL_pairs LOD score 3.58). Nominal or suggestive evidence of linkage to this locus was also detected when the three populations were analyzed separately. Suggestive evidence of linkage was found to six additional loci in the Finnish and French sample sets.

Conclusions

This study identified a novel DN locus at chromosome 22q11 with significant evidence of linkage to DN. Our results suggest that this locus may be of importance in European populations. In addition, this study supports previously indicated DN loci on 3q21–q25 and 19q13.