Food encounter rate of simulated termite tunnels in heterogeneous landscapes

The aim of this study was to explore how a heterogeneous landscape affects food encounter rate in the Formosan subterranean termite, Coptotermes formosanus Shiraki. To do this, a lattice model was formulated to simulate the tunneling structure of the termite. The model made use of minimized local rules derived from empirical data. In addition, a landscape structure was generated on a lattice space by using a neutral landscape model. Each lattice cell has a value h, representing spatially distributed property of the landscape (e.g., temperature or moisture). The heterogeneity of the landscape was characterized by a parameter, H controlling aggregation of lattice cells with higher values of h. Higher H values correspond to higher aggregation levels. The effect of the landscape heterogeneity on the encounter rate was clear in the presence of higher food density than in lower density. The effect was also enhanced by the increase of the number of primary tunnels.     

Serum-free solutions for cryopreservation of cells

With the development of cell-based assays and therapies, the purity of reagents used to grow and maintain cells has become much more important. In particular, the use of fetal calf serum for culturing cells presents a direct path for potential contamination of cell cultures. In recent years, much research has focused on the development of serum-free culturing systems, not only to alleviate difficulties due to availability and cost of fetal calf serum but also to prevent the transmission of potentially fatal diseases to human patients. Additionally, methods need to be developed for long-term storage of cell stocks that also reduce the risk of exposure to harmful diseases. As most methods employ fetal calf serum in their freezing formulations, solutions that avoid the use of fetal calf serum while providing equivalent or better recovery of cells upon thawing would be ideal. In this study, two vascular cell lines have been cryopreserved as adherent cell populations in two widely used cryoprotectants, dimethyl sulfoxide and 1,2-propanediol, and two vehicle solutions, Euro-Collins and Unisol-cryoprotectant vehicle specifically formulated for the maintenance of cell homeostasis at temperatures below 37° C. The addition of serum to these formulations was also evaluated to determine if its presence provided any additional benefit to the cells during cryopreservation. The results demonstrated that using vehicle solutions designed for lower temperatures produced viable cells that retained cell population viability values up to 75% of unfrozen controls. These results also demonstrated that including serum in the formulation provided no additional benefit to the cells and in some cases actually produced lower cell viability after cryopreservation. In conclusion, the development of solutions designed for low-temperature storage of cells provides a viable alternative to more conventional cryopreservation protocols and eliminates the necessity of including serum in these formulations.     

A novel bacterial community index to assess stream ecological health

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CAERUS: predicting CAncER oUtcomeS using relationship between protein structural information, protein networks, gene expression data, and mutation data

Carcinogenesis is a complex process with multiple genetic and environmental factors contributing to the development of one or more tumors. Understanding the underlying mechanism of this process and identifying related markers to assess the outcome of this process would lead to more directed treatment and thus significantly reduce the mortality rate of cancers. Recently, molecular diagnostics and prognostics based on the identification of patterns within gene expression profiles in the context of protein interaction networks were reported. However, the predictive performances of these approaches were limited. In this study we propose a novel integrated approach, named CAERUS, for the identification of gene signatures to predict cancer outcomes based on the domain interaction network in human proteome. We first developed a model to score each protein by quantifying the domain connections to its interacting partners and the somatic mutations present in the domain. We then defined proteins as gene signatures if their scores were above a preset threshold. Next, for each gene signature, we quantified the correlation of the expression levels between this gene signature and its neighboring proteins. The results of the quantification in each patient were then used to predict cancer outcome by a modified naïve Bayes classifier. In this study we achieved a favorable accuracy of 88.3%, sensitivity of 87.2%, and specificity of 88.9% on a set of well-documented gene expression profiles of 253 consecutive breast cancer patients with different outcomes. We also compiled a list of cancer-associated gene signatures and domains, which provided testable hypotheses for further experimental investigation. Our approach proved successful on different independent breast cancer data sets as well as an ovarian cancer data set. This study constitutes the first predictive method to classify cancer outcomes based on the relationship between the domain organization and protein network.     

A novel RING finger protein, Znf179, modulates cell cycle exit and neuronal differentiation of P19 embryonal carcinoma cells

Znf179 is a member of the RING finger protein family. During embryogenesis, Znf179 is expressed in a restricted manner in the brain, suggesting a potential role in nervous system development. In this report, we show that the expression of Znf179 is upregulated during P19 cell neuronal differentiation. Inhibition of Znf179 expression by RNA interference significantly attenuated neuronal differentiation of P19 cells and a primary culture of cerebellar granule cells. Using a microarray approach and subsequent functional annotation analysis, we identified differentially expressed genes in Znf179-knockdown cells and found that several genes are involved in development, cellular growth, and cell cycle control. Flow cytometric analyses revealed that the population of G0/G1 cells decreased in Znf179-knockdown cells. In agreement with the flow cytometric data, the number of BrdU-incorporated cells significantly increased in Znf179-knockdown cells. Moreover, in Znf179-knockdown cells, p35, a neuronal-specific Cdk5 activator that is known to activate Cdk5 and may affect the cell cycle, and p27, a cell cycle inhibitor, also decreased. Collectively, these results show that induction of the Znf179 gene may be associated with p35 expression and p27 protein accumulation, which lead to cell cycle arrest in the G0/G1 phase, and is critical for neuronal differentiation of P19 cells.     

Lessons from nature for preservation of mammalian cells, tissues, and organs

The study of mechanisms by which animals tolerate environmental extremes may provide strategies for preservation of living mammalian materials. Animals employ a variety of compounds to enhance their survival, including production of disaccharides, glycerol, and antifreeze compounds. The cryoprotectant glycerol was discovered before its role in amphibian survival. In the last decade, trehalose has made an impact on freezing and drying methods for mammalian cells. Investigation of disaccharides was stimulated by the variety of organisms that tolerate dehydration stress by accumulation of disaccharides. Several methods have been developed for the loading of trehalose into mammalian cells, including inducing membrane lipid-phase transitions, genetically engineered pores, endocytosis, and prolonged cell culture with trehalose. In contrast, the many antifreeze proteins (AFPs) identified in a variety of organisms have had little impact. The first AFPs to be discovered were found in cold water fish; their AFPs have not found a medical application. Insect AFPs function by similar mechanisms, but they are more active and recombinant AFPs may offer the best opportunity for success in medical applications. For example, in contrast to fish AFPs, transgenic organisms expressing insect AFPs exhibit reduced ice nucleation. However, we must remember that nature's survival strategies may include production of AFPs, antifreeze glycolipids, ice nucleators, polyols, disaccharides, depletion of ice nucleators, and partial desiccation in synchrony with the onset of winter. We anticipate that it is only by combining several natural low temperature survival strategies that the full potential benefits for mammalian cell survival and medical applications can be achieved.     

Genetic diversity and widespread haplotypes in a migratory dragonfly, the common green darner Anax junius

Abstract.  1. Species that undertake regular two-way migration may be expected, through population connectivity, to exhibit some level of genetic similarity over broad spatial scales. Although seldom following two-way migration, highly mobile insect species tend to exhibit either low haplotype diversity and no phylogeographic structuring, or relatively high haplotype diversity and pronounced phylogeographic structuring.
2. This study reveals the first wide-scale genetic characterisation of a migratory dragonfly, the common green darner Anax junius Drury. Unusually for insects, north-south two-way migration is common in this species, although not obligatory. In at least part of its range, some individuals follow an extended developmental period and overwinter in a state of diapause.
3. Mitochondrial sequence data were obtained from 92  A. junius individuals collected from 35 sites across Canada, U.S.A., and Mexico. These revealed 38 haplotypes, some of which were extremely widespread, although the majority (27 haplotypes) was found in only one individual. In contrast to previous studies on mobile insects, the overall pattern was of relatively high haplotype diversity in the absence of phylogeographic structuring.
4. Migrants and non-migrants, which sometimes shared haplotypes, were distributed across multiple genetic lineages. This suggests that, contrary to some earlier assertions, developmental pathways in this species may be plastic. Such plasticity would allow highly mobile species to adapt to a range of environmental conditions, and may be key to the widespread distribution of multiple haplotypes.     

Editorial

There are occasionally times when I feel that the field of proteomicsis a mixed blessing. The promise of the field is clear and thetechnologies for measuring, quantifying and characterizing proteinsfrom living systems are evolving rapidly and leading to newbiological paradigms. On the other hand, there are many examplesof research