A review of non-invasive optical-based image analysis systems for continuous bioprocess monitoring

To observe and control cultivation processes, optical sensors are used increasingly. Important variables for controlling such processes are cell count, cell size distribution and the morphology of cells. Among turbidity measurement methods, imaging procedures are applied for determining these process values. A disadvantage of most previously developed imaging procedures is that they are only available offline, which requires sampling. On the other hand, available imaging inline probes can only deliver a limited number of process values so far. This contribution gives an overview of optical procedures for the inline determination of cell count, cell size distribution and other variables. In particular, by in situ microscopy, an imaging procedure will be described, which allows the determination of direct and non-direct cell variables in real time without sampling.     

Differential effects of nutrient-limited primary production on primary, secondary or tertiary consumers

Nutritional imbalances between predator and prey are the rule rather than the exception at the lower end of food webs. We investigated the role of different grazers in the propagation of nutritionally imbalanced primary production by using the same primary producers in a three-trophic-level food chain and a four-trophic-level food chain experimental setup. The three-trophic-level food chain consisted of a classic single-cell primary producer (Rhodomonas salina), a metazoan grazer (the copepod Acartia tonsa) and a top predator (the jellyfish Gonionemus vertens), while we added a protozoan grazer (Oxyrrhis marina) as primary consumer to the food chain to establish the four-trophic-level food chain. This setup allowed us to investigate how nutrient-limitation effects change from one trophic level to another, and to investigate the performance of two components of our experimental food chains in different trophic positions. Stoichiometry and fatty acid profiles of the algae showed significant differences between the nutrient-depleted [no N and no P addition (?P), respectively] and the nutrient-replete (f/2) treatments. The differences in stoichiometry could be traced when O. marina was the first consumer. Copepods feeding on these flagellates were not affected by the nutritional imbalance of their prey in their stoichiometry, their respiration rates nor in their developmental rates. In contrast, when copepods were the primary consumer, those reared on the ?P algae showed significantly higher respiration rates along with significantly lower developmental rates. In neither of our two experimental food chains did the signals from the base of the food chains travel up to jelly fish, our top predator.     

20th International Symposium on Shiftwork and Working Time: biological mechanisms, recovery, and risk management in the 24-h society

This dedicated issue of Chronobiology International is devoted to the selected proceedings of the 20th International Symposium on Shift Work and Working Time held in Stockholm, Sweden, 28 June to 1 July 2011. It constitutes the fifth such issue of the journal since 2004 dedicated to the selected proceedings to the meetings of the Working Time Society. The key theme of the 20th Symposium was "Biological Mechanisms, Recovery, and Risk Management in the 24-h Society." The collection of papers of this dedicated issue represents the best of contemporary research on the effects of night and rotating shift schedules on worker health and safety. The contents cover such topics as sleep restriction, injuries, health, and performance of night work and rotating shiftwork, plus light treatment as a countermeasure against the circadian disruption of shiftwork. The majority of the papers are observational field studies, including some of large sample size, and three studies are well-designed laboratory experiments.     

Gender differences in inflammatory proteins and pathways in seasonal allergic rhinitis

In model organisms, thousands of genes differ in expression between females and males. It is not known if differences on a similar scale are found in humans nor how this relates to disease. However, in allergic disease gender differences in the levels of both inflammatory cells and proteins have been shown. In this study, we found lower nasal fluid allergen-specific IgE in women than men with seasonal allergic rhinitis (SAR). This led to genome-wide analyses of gene expression in allergen-challenged CD4⁺ cells from patients with SAR before and after treatment with cortisone. Before treatment, 975 genes differed in expression between women and men: 337 were higher in women. After treatment only 428 genes and one pathway differed in expression. The genes that differed in expression between women and men were over-represented in 10 pathways. Five of the pathways regulated chemotaxis. All five were less active in women. One of the pathways was induced by the eosinophilic chemokine CCL4. Analysis of nasal fluid CCL4 protein confirmed lower levels in women with seasonal allergic rhinitis, before and during the pollen season. By contrast, nasal fluid CCL3 levels did not differ between the genders. In summary, this study shows gender differences in specific inflammatory pathways and proteins in patients with seasonal allergic rhinitis. Further studies are warranted to examine if such differences have diagnostic and therapeutic implications in allergic diseases.     

Changes in light- and nitrogen-use and in aboveground biomass allocation patterns along productivity gradients in grasslands

Light- and nitrogen-use change was examined along productivity gradients in natural grasslands at Laelatu, western Estonia, both at community level and in most abundant species. Aboveground biomass (M) ranged from 341 to 503 g m^?2 in wet (W) and from 248 to 682 g m^?2 in dry (D) community. Aboveground leaf area ratio (aLAR) decreased with rising M in D site, while it increased in W site. In a high-aLAR W community (significantly higher compared to D), adjustment of leaf morphology through an increase in specific leaf area is responsible for an increase in aLAR with rising productivity. In low-aLAR stand, by contrast, adjustment of biomass allocation due to decrease in aboveground leaf mass fraction is primarily responsible for the tendency of aLAR to decline. In conclusion, a decrease in aLAR is not a universal response to increasing M. We hypothesise that there exists an optimum of light acquisition efficiency (Φ_M) along a productivity gradient independent of community type. Aboveground nitrogen-use efficiency (aNUE) decreased in high-aLAR, W community with increasing M, while in low-aLAR, D site, there was no relationship along a gradient, although aNUE increased along six plots dominated by graminoids. A trade-off was established between leaf nitrogen content per unit leaf area (N _A) and aLAR.     

Pest species diversity enhances control of spider mites and whiteflies by a generalist phytoseiid predator

To test the hypothesis that pest species diversity enhances biological pest control with generalist predators, we studied the dynamics of three major pest species on greenhouse cucumber: Western flower thrips, Frankliniella occidentalis (Pergande), greenhouse whitefly, Trialeurodes vaporariorum (Westwood), and two-spotted spider mites, Tetranychus urticae Koch in combination with the predator species Amblyseius swirskii Athias-Henriot. When spider mites infested plants prior to predator release, predatory mites were not capable of controlling spider mite populations in the absence of other pest species. A laboratory experiment showed that predators were hindered by the webbing of spider mites. In a greenhouse experiment, spider mite leaf damage was lower in the presence of thrips and predators than in the presence of whiteflies and predators, but damage was lowest in the presence of thrips, whiteflies and predators. Whitefly control was also improved in the presence of thrips. The lower levels of spider mite leaf damage probably resulted from (1) a strong numerical response of the predator (up to 50 times higher densities) when a second and third pest species were present in addition to spider mites, and (2) from A. swirskii attacking mobile spider mite stages outside or near the edges of the spider mite webbing. Interactions of spider mites with thrips and whiteflies might also result in suppression of spider mites. However, when predators were released prior to spider mite infestations in the absence of other pest species, but with pollen as food for the predators, we found increased suppression of spider mites with increased numbers of predators released, confirming the role of predators in spider mite control. Thus, our study provides evidence that diversity of pest species can enhance biological control through increased predator densities.     

Contributions of the EMERALD project to assessing and improving microarray data quality

While minimum information about a microarray experiment (MIAME) standards have helped to increase the value of the microarray data deposited into public databases like ArrayExpress and Gene Expression Omnibus (GEO), limited means have been available to assess the quality of this data or to identify the procedures used to normalize and transform raw data. The EMERALD FP6 Coordination Action was designed to deliver approaches to assess and enhance the overall quality of microarray data and to disseminate these approaches to the microarray community through an extensive series of workshops, tutorials, and symposia. Tools were developed for assessing data quality and used to demonstrate how the removal of poor-quality data could improve the power of statistical analyses and facilitate analysis of multiple joint microarray data sets. These quality metrics tools have been disseminated through publications and through the software package arrayQualityMetrics. Within the framework provided by the Ontology of Biomedical Investigations, ontology was developed to describe data transformations, and software ontology was developed for gene expression analysis software. In addition, the consortium has advocated for the development and use of external reference standards in microarray hybridizations and created the Molecular Methods (MolMeth) database, which provides a central source for methods and protocols focusing on microarray-based technologies.     

Effects of hyperactive Janus kinase 2 signaling in mammary epithelial cells

Ornithine decarboxylase (ODC), the first rate-limiting enzyme in the polyamine biosynthesis is one of the most rapidly degraded proteins in eukaryotic cells. Mammalian ODC is a notable exception to the widely accepted dogma that ubiquitination is always required for targeting a protein to degradation by the 26S proteasome. However, while it is well established that in mammalian cells degradation of ODC is ubiquitin independent, the requirement of ubiquitination for degradation of ODC in yeast cells remained undetermined. We have investigated ODC degradation in three mutant strains of Saccharomyces cerevisiae in which ubiquitin-dependent protein degradation activity is severely compromised. While yeast ODC was rapidly degraded in all these mutant strains the degradation of N-end rule substrates was inhibited. A mutant mouse ODC that fails to interact with Az was rapidly degraded in yeast cells but was stable in mammalian cells suggesting that interaction with a mammalian Az like yeast protein is not necessary for the degradation of ODC in yeast cells. Deletion analysis revealed that sequences from its unique N-terminus are involved in targeting yeast ODC to rapid degradation in yeast cells.     

Ectoparasite intensities are correlated with endoparasite infection loads in willow ptarmigan

Most studies exploring the effect of parasites on host fitness traits deal with a small subset of the parasite community, or with a single parasite species. The results of such studies may be difficult to interpret, because the potential effects of other parasites are not controlled for. If intensities of different parasite species tend to covary, any demonstrated effect by one parasite species could be caused by another, covarying species. In the current study we found that intensities of two different feather lice on willow ptarmigan were positively correlated. Moreover, ectoparasite intensities could be reliably predicted by endoparasite loads. This is unexpected since feather lice are controlled by preening, while endoparasites are kept in check by the immune system. Our results suggest a link between these two aspects of parasite defense, possibly mediated by endoparasite infections reducing host energy available for preening.