Phospholipid characteristics and neutral lipid fatty acid composition related to temperature and nutritional conditions in ecologically important amphipod species from the northern Baltic Sea

Lipid composition of the benthic, stenothermal amphipod Monoporeia affinis collected from constantly cold deep-water (> 80 m) regions of the northern Baltic Sea was analysed in detail to study phospholipid characteristics, its relation to thermal adaptation as well as potential effects of food quality and seasonal variability. Similar measurements were performed on the littoral, eurythermic amphipod Gammarus spp. Fatty acid (FA) composition of storage lipids of Pontoporeia femorata, a sibling species of M. affinis, was also studied. Interannual and interspecies variability in selected FA was observed both in triacylglycerols (TAG) and phospholipids (PL). Differences in monounsaturated vs. polyunsaturated (MUFA/PUFA) FA combinations of phosphatidyl ethanolamine (PE) diacyl and alkylacyl subgroups were also observed. Seasonal variability in M. affinis was considerably lesser compared to Gammarus spp. A literature synopsis shows that in diacyl PE the share of the FA combination MUFA/PUFA increases with lowering body temperature (40-55% in cold-adapted organisms vs. 5-15% in warm adapted ones), signifying that this characteristic is probably in key position concerning regulation of membrane fluidity in temperature adaptation. According to this feature M. affinis belongs to the group of cold-adapted stenothermic species (Group 1) while eurythermic Gammarus spp. settles in the Group 2 (cold-acclimatized) or 3 (warm-acclimatized/tropical) depending on the status of temperature adaptation. Omnivory and/or periodical food item switching is an important strategy in benthic organisms in high-latitude areas characterised by recurring long poor-nutritional periods. Since many benthic species utilise a time-averaged, integrated food source from phytal and animal matter from various sources the FA composition of TAG of the amphipod species measured here do not exclusively point towards any specific feeding mode or food source. In general, using selected FA as food source markers to assess the diet of field collected more-or-less omnivoric species cannot be considered as an optimal approach. The current study gives more insight to the biochemistry of biological membranes of aquatic crustaceans that is essential in estimation of the capacity of the thermal adaptation/acclimatization of organisms as well as the potential effects of food quality on storage lipids.     

Rapid sympatric ecological differentiation of crater lake cichlid fishes within historic times

Background  

After a volcano erupts, a lake may form in the cooled crater and become an isolated aquatic ecosystem. This makes fishes in crater lakes informative for understanding sympatric evolution and ecological diversification in barren environments. From a geological and limnological perspective, such research offers insight about the process of crater lake ecosystem establishment and speciation. In the present study we use genetic and coalescence approaches to infer the colonization history of Midas cichlid fishes (Amphilophus cf. citrinellus) that inhabit a very young crater lake in Nicaragua-the ca. 1800 year-old Lake Apoyeque. This lake holds two sympatric, endemic morphs of Midas cichlid: one with large, hypertrophied lips (~20% of the total population) and another with thin lips. Here we test the associated ecological, morphological and genetic diversification of these two morphs and their potential to represent incipient speciation.     

Epithelial N-cadherin and nuclear β-catenin are up-regulated during early development of human lung

Background  

The aim of this study was to analyze the cell-specific expression of E- and N-cadherin and β-catenin in developing human lung tissues from 12 to 40 weeks of gestation.     

Quantification of lysophosphatidic acids in rat brain tissue by liquid chromatography–electrospray tandem mass spectrometry

Lysophosphatidic acid (LPA) is a lipid mediator with multiple biological functions. A highly selective and sensitive liquid chromatography–tandem mass spectrometry (LC/MS/MS) method was developed for the determination of LPAs (16:0 LPA, 18:0 LPA, 18:1 LPA, 20:4 LPA) in rat brain cryosections. After partitioning the LPAs from other lipophilic material present in the tissue with a liquid–liquid extraction, a reversed-phase column and ion pair technique was used for separating analytes with a gradient elution. An internal standard (17:0 LPA) was included in the analysis. Detection and quantification of the LPAs were carried out with a triple quadrupole mass spectrometer using negative electrospray ionization (ESI) and multiple reaction monitoring (MRM). The artificial formation of LPAs from lysophosphatidylcholines during the sample preparation procedure and instrumentation was carefully studied during the method development. The method was validated; acceptable selectivity, accuracy, precision, recovery, and stability were obtained for concentrations within the calibration curve range of 0.02–1.0 μM for LPAs. The quantification limit of the assay was 54 fmol injected into column for each LPAs. The method was applied to comparative studies of LPA levels in rat brain cryosections after the various chemical pre-treatments of the sections.     

Phenotypic characters of static homology increase phylogenetic stability under direct optimization of otherwise dynamic homology characters

Direct optimization of unaligned sequence characters provides a natural framework to explore the sensitivity of phylogenetic hypotheses to variation in analytical parameters. Phenotypic data, when combined into such analyses, are typically analyzed with static homology correspondences unlike the dynamic homology sequence data. Static homology characters may be expected to constrain the direct optimization and thus, potentially increase the similarity of phylogenetic hypotheses under different cost sets. However, whether a total-evidence approach increases the phylogenetic stability or not remains empirically largely unexplored. Here, I studied the impact of static homology data on sensitivity using six empirical data sets composed of several molecular markers and phenotypic data. The inclusion of static homology phenotypic data increased the average stability of phylogenetic hypothesis in five out of the six data sets. To investigate if any static homology characters would have similar effect, the analyses were repeated with randomized phenotypic data, and with one of the molecular markers fixed as static homology characters. These analyses had, on average, almost no effect on the phylogenetic stability, although the randomized phenotypic data sometimes resulted in even higher stability than empirical phenotypic data. The impact was related to the strength of the phylogenetic signal in the phenotypic data: higher average jackknife support of the phenotypic tree correlated with stronger stabilizing effect in the total-evidence analysis. Phenotypic data with a strong signal made the total-evidence trees topologically more similar to the phenotypic trees, thus, they constrained the dynamic homology correspondences of the sequence data. Characters that increase phylogenetic stability are particularly valuable for phylogenetic inference. These results indicate an important role and additive value of phenotypic data in increasing the stability of phylogenetic hypotheses in total-evidence analyses.     

Probabilistic Prediction of Contacts in Protein-Ligand Complexes

We introduce a statistical method for evaluating atomic level 3D interaction patterns of protein-ligand contacts. Such patterns can be used for fast separation of likely ligand and ligand binding site combinations out of all those that are geometrically possible. The practical purpose of this probabilistic method is for molecular docking and scoring, as an essential part of a scoring function. Probabilities of interaction patterns are calculated conditional on structural x-ray data and predefined chemical classification of molecular fragment types. Spatial coordinates of atoms are modeled using a Bayesian statistical framework with parametric 3D probability densities. The parameters are given distributions a priori, which provides the possibility to update the densities of model parameters with new structural data and use the parameter estimates to create a contact hierarchy. The contact preferences can be defined for any spatial area around a specified type of fragment. We compared calculated contact point hierarchies with the number of contact atoms found near the contact point in a reference set of x-ray data, and found that these were in general in a close agreement. Additionally, using substrate binding site in cathechol-O-methyltransferase and 27 small potential binder molecules, it was demonstrated that these probabilities together with auxiliary parameters separate well ligands from decoys (true positive rate 0.75, false positive rate 0). A particularly useful feature of the proposed Bayesian framework is that it also characterizes predictive uncertainty in terms of probabilities, which have an intuitive interpretation from the applied perspective.     

Teratocarcinoma stem cells as a model for differentiation in the mouse embryo

Embryonal carcinoma (EC) cells, which are the malignant stem cells of teratocarcinomas, are considered similar to early embryo cells. The EC cells can be grown in vitro, and many of them can be experimentally induced to differentiate; upon differentiation, the cells become benign. Here we review some of the changes that take place in the cellular and molecular characteristics of murine F9 EC cells as they differentiate into endodermal cells. Upon differentiation of F9 cells, distinct changes occur in their cell surface molecules, cytoskeleton-associated proteins and cell adhesion properties. Simultaneously, the rate of cell proliferation decreases due to a dramatic increase in duration of G1 and S phases of the cell cycle. The changes in gene expression and cell behavior occurring during endodermal differentiation of EC cells closely resemble those occurring when the endoderm differentiates in the embryo. Teratocarcinoma stem cell lines may thus be exploited to enhance understanding of both teratoma-type neoplasms and embryonic development.     

Action of cytochalasin B on cytoplasmic streaming systems and morphogenesis in Micrasterias torreyi (Conjugatophyceae)

The effects of cytochalasin B on the development and morphology of the Micrasterias cell vary according to different developmental stages. CB (especially 5–6 μm/ml) does not stop the growth of a developing semicell during early developmental stages and allows the formation of a three–lobed form, which is a kind of a basic form preceding the actual morphogenesis, further growth and development still being totally prevented by the same concentration. This is due to the occurrence of two separate cytoplasmic streaming systems in the developing semicell, one being cortical, more CB sensitive, the other being more central, not as sensitive to CB, both being microfilament based. The cortical streaming system supports tip growth, and many observations indicate that this system is also associated with the intermediation of the nuclear control regulating morphogenesis in Micrasterias. The effects of CB are specific: it has not been found to have distinct effects on the ultrastructure of the cell, on cell wall material production, or on the turgor pressure of the cell.