Immune Response Modeling of Interferon β-Pretreated Influenza Virus-Infected Human Dendritic Cells

The pretreatment of human dendritic cells with interferon-β enhances their immune response to influenza virus infection. We measured the expression levels of several key players in that response over a period of 13 h both during pretreatment and after viral infection. Their activation profiles reflect the presence of both negative and positive feedback loops in interferon induction and interferon signaling pathway. Based on these measurements, we have developed a comprehensive computational model of cellular immune response that elucidates its mechanism and its dynamics in interferon-pretreated dendritic cells, and provides insights into the effects of duration and strength of pretreatment.     

Co-occurrence of ectoparasites on rodent hosts: null model analyses of data from three continents

We studied patterns of species co-occurrence in communities of ectoparasitic arthropods (ixodid ticks, mesostigmate mites and fleas) harboured by rodent hosts from South Africa ( Rhabdomys pumilio ), South America ( Scapteromys aquaticus and Oxymycterus rufus ) and west Siberia ( Apodemus agrarius , Microtus gregalis , Microtus oeconomus and Myodes rutilus ) using null models. We compared frequencies of co-occurrences of parasite species or higher taxa across host individuals with those expected by chance. When non-randomness of parasite co-occurrences was detected, positive but not negative co-occurrences of parasite species or higher taxa prevailed (except for a single sample of mesostigmate mites from O. rufus ). Frequency of detection of non-randomness of parasite co-occurrences differed among parasite taxa, being higher in fleas and lower in mites and ticks. This frequency differed also among host species independent of parasite taxon, being highest in Microtus species and lowest in O. rufus and S. aquaticus . We concluded that the pattern of species co-occurrence in ectoparasite communities on rodent hosts is predominantly positive, depends on life history of parasites and may be affected to a great extent by life history of a host.     

The production and scavenging of reactive oxygen species in the plastoquinone pool of chloroplast thylakoid membranes

Reactive oxygen species (ROS) resulting from oxygen reduction, superoxide anion radical O and hydrogen peroxide H ₂O₂ are very significant in the cell metabolism of aerobic organisms. They can be destructive and lead to apoptosis and they can also serve as signal molecules. In the light, chloroplasts are known to be one of the main sources of ROS in plants. However, the components involved in oxygen reduction and the detailed chemical mechanism are not yet well established. The present review describes the experimental data and theoretical considerations that implicate the plastoquinone pool (PQ‐pool) in this process. The evidence indicates that the PQ‐pool has a dual role: (1) the reduction of O₂ by plastosemiquinone to superoxide and (2) the reduction of superoxide by plastohydroquinone to hydrogen peroxide. The second role represents not only the scavenging of superoxide, but also the generation of hydrogen peroxide as an important signaling molecule. The regulatory and protective functions of the PQ‐pool are discussed in the context of these reactions.     

Docking of calcium ions in proteins with flexible side chains and deformable backbones

A method of docking Ca²⁺ ions in proteins with flexible side chains and deformable backbones is proposed. The energy was calculated with the AMBER force field, implicit solvent, and solvent exposure-dependent and distance-dependent dielectric function. Starting structures were generated with Ca²⁺ coordinates and side-chain torsions sampled in 1000 Å³ cubes centered at the experimental Ca²⁺ positions. The energy was Monte Carlo-minimized. The method was tested on fourteen Ca²⁺-binding sites. For twelve Ca²⁺-binding sites the root mean square (RMS) deviation of the apparent global minimum from the experimental structure was below 1.3 and 1.7 Å for Ca²⁺ ions and side-chain heavy atoms, respectively. Energies of multiple local minima correlate with the RMS deviations from the X-ray structures. Two Ca²⁺-binding sites at the surface of proteinase K were not predicted, because of underestimation of Ca²⁺ hydration energy by the implicit-solvent method.     

Critical role for hyperpolarization-activated cyclic nucleotide-gated channel 2 in the AIF-mediated apoptosis

Cellular calcium uptake is a controlled physiological process mediated by multiple ion channels. The exposure of cells to either one of the protein kinase C (PKC) inhibitors, staurosporine (STS) or PKC412, can trigger Ca²⁺ influx leading to cell death. The precise molecular mechanisms regulating these events remain elusive. In this study, we report that the PKC inhibitors induce a prolonged Ca²⁺ import through hyperpolarization‐activated cyclic nucleotide‐gated channel 2 (HCN2) in lung carcinoma cells and in primary culture of cortical neurons, sufficient to trigger apoptosis‐inducing factor (AIF)‐mediated apoptosis. Downregulation of HCN2 prevented the drug‐induced Ca²⁺ increase and subsequent apoptosis. Importantly, the PKC inhibitors did not cause Ca²⁺ entry into HEK293 cells, which do not express the HCN channels. However, introduction of HCN2 sensitized them to STS/PKC412‐induced apoptosis. Mutagenesis of putative PKC phosphorylation sites within the C‐terminal domain of HCN2 revealed that dephosphorylation of Thr⁵⁴⁹ was critical for the prolonged Ca²⁺ entry required for AIF‐mediated apoptosis. Our findings demonstrate a novel role for the HCN2 channel by providing evidence that it can act as an upstream regulator of cell death triggered by PKC inhibitors.     

The steroid glycoside H.g.-12 from Hoodia gordonii activates the human bitter receptor TAS2R14 and induces CCK release from HuTu-80 cells

Steroid glycosides extracted from the succulent plant Hoodia gordonii are suggested to have appetite-suppressant effects both in animals and humans. Yet, the mechanisms underlying the putative satiety action of Hoodia steroid glycosides are not fully understood. We found that H.g.-12, a steroid glycoside purified from H. gordonii extract, initiated cholecystokinin (CCK) secretion both ex vivo in rat intestine and in vitro in the human enteroendocrine (EC) cell line HuTu-80. CCK is known to exert central effects on appetite suppression via the vagus nerve which afferents terminate in the gut wall. Recent data show that G protein-coupled receptors signaling bitter taste (T2Rs) are expressed in both rodent and human gastrointestinal tract. It was further demonstrated that bitter sensing is functional in mouse STC-1 EC cells and leads to CCK secretion via increased intracellular Ca2(+) concentrations. Based on the bitter taste of H. gordonii purified extracts, we assessed whether H.g.-12 could activate human bitter receptors. The steroid glycoside activated selectively TAS2R7 and TAS2R14, both heterologously expressed in HEK 293 cells. Removing an essential structural feature from the steroid glycoside inhibited H.g.-12-induced Ca2(+) increase in TAS2R14-expressing HEK cells and abolished H.g.-12-induced CCK secretion from human EC cells. Similarly, a nonspecific bitter receptor antagonist abolished H.g.-12-induced CCK secretion in HuTu-80 cells. These results point to a potential route of action by which components of Hoodia might influence appetite control. Our data also provide additional evidence that bitter taste-sensing mechanisms are coupled to hormone release from EC cells in the intestine. Moreover, we identified a natural agonist of TAS2R7 and TAS2R14 for further studies on the role of bitter receptors in satiety control and food intake.     

Evaluating the sampling bias in pattern of subterranean species richness: combining approaches

We investigated the pattern of species richness of obligate subterranean (troglobiotic) beetles in caves in the northwestern Balkans, given unequal and biased sampling. On the regional scale, we modeled the relationship between species numbers and sampling intensity using an asymptotic Clench (Michaelis–Menten) function. On the local scale, we calculated Chao 2 species richness estimates for 20 × 20 km grid cells, and investigated the distribution of uniques, species found in only one cave within the grid cell. Cells having high positive residuals, those with above average species richness than expected according to the Clench function, can be considered true hotspots. They were nearly identical to the observed areas of highest species richness. As sampling intensity in a grid cell increases the expected number of uniques decreases for any fixed number of species in the grid cell. High positive residuals show above average species richness for a certain level of sampling intensity within a cell, so further sampling has the most potential for additional species. In some cells this was supported by high numbers of uniques, also indicating insufficient sampling. Cells with low negative residuals have fewer species than would be expected, and some of them also had a low number of uniques, both indicating sufficient sampling. By combining different analyses in a novel way we were able to evaluate observed species richness pattern as well as identify, where further sampling would be most beneficial. Approach we demonstrate is of broad interest to study of biota with high levels of endemism, small distribution ranges and low catchability.     

Inflammation in fetal sheep from intra-amniotic injection of Ureaplasma parvum

Bronchopulmonary dysplasia is associated with chorioamnionitis and fetal lung inflammation. Ureaplasma species are the bacteria most frequently isolated from chorioamnionitis. Very chronic ureaplasma colonization of amniotic fluid causes low-grade lung inflammation and functional lung maturation in fetal sheep. Less is known about shorter exposures of the fetal lung. Therefore, we hypothesized that ureaplasmas would cause an acute inflammatory response that would alter lung development. Singleton ovine fetuses received intra-amniotic Ureaplasma parvum serovar 3 or control media at 110, 117, or 121 days and were delivered at 124 days gestational age (term = 150 days). Inflammation was assessed by 1) cell counts in bronchoalveolar lavage fluid (BALF), and 2) cytokine mRNA measurements, immunohistochemistry, and flow cytometry for inflammatory cells and elastin and α-smooth muscle actin (α-SMA) staining in lung tissue. Neutrophils were increased in BALF 3 days after exposure to ureaplasmas (P = 0.01). Myeloperoxidase-positive cells increased after 3 days (P = 0.03), and major histocompatibility complex (MHC) class II-positive cells increased after 14 days of ureaplasma exposure (P = 0.001). PU.1 (macrophage marker)- or CD3 (T lymphocyte marker)-positive cells were not induced by ureaplasmas. CD3-positive cells in the posterior mediastinal lymph node increased in ureaplasma-exposed animals at 3, 7, and 14 days (P = 0.002). Focal elastin depositions decreased in alveolar septa at 14 days (P = 0.002), whereas α-SMA increased in arteries and bronchioli. U. parvum induced a mild acute inflammatory response and changed elastin and α-SMA deposition in the lung, which may affect lung structure and subsequent development.     

Old museum samples and recent taxonomy: A taxonomic,biogeographic and conservation perspective of the <Emphasis Type="Italic">Niphargus tatrensis</Emphasis> species complex (Crustacea: Amphipoda)

Natural history museum collections harbour valuable information on species. The usefulness of such data critically depends on the accurate identification of species, which has been challenged by introduction of molecular techniques into taxonomy. However, most collections may suffer from DNA degradation, due to age and/or improper preservation; hence the identification of specimens depends solely on morphological features. This study explores how and to what extent morphological data can help to solve ambiguous taxonomic cases based on selected species concepts and with the use of operational criteria in a species-hypothesis testing procedure. The studied taxon, the Niphargus tatrensis species complex, comprises freshwater subterranean amphipods, distributed across Central Europe, the taxonomic status of which was debated extensively between 1930 and 1960. Using the general species concept, character- and tree-based operational criteria reveal northern and southern diagnosable and exclusive lineages identified here as N. tatrensis Wrześniowski, 1888 and N. scopicauda sp. n., respectively. The remaining populations represent the non-exclusive N. aggtelekiensis Dudich, 1932, which occurs from the eastern Alps to Hungary. In the entire complex, altitudinal distribution is largely limited to areas above 400 m, where the mean annual temperature never exceeds 9°C. Seemingly well-defined distributional ranges of N. tatrensis and N. aggtelekiensis are fragmented in an ecological sense, which raises the question whether two of the three species recognised here actually consist of several unidentified taxa. Morphological similarity between the species, numerous polymorphic features, and the association with cool temperatures lead to a hypothesis in which fragmentation of the ancestral range occurred during post-Pleistocene climate warming, reducing gene flow across lowland populations due to niche conservatism of the ancestral species and/or to invasion of competitive species along the Danube and Drava rivers. The results are discussed regarding how old museum samples are conducive to more detailed molecular-taxonomic and conservation studies.