Genetic differentiation of European grayling (Thymallus thymallus) populations in Serbia,based on mitochondrial and nuclear DNA analyses

Background

The structure and diversity of grayling (Thymallus thymallus) populations have been well studied in most of its native habitat; however the southernmost populations of the Balkan Peninsula remain largely unexplored. The purpose of this study was to assess the genetic diversity of Serbian grayling populations, detect the impact of stocking and provide guidelines for conservation and management.

Methods

Eighty grayling individuals were collected from four rivers (Ibar, Lim, Drina and Rzav). The mitochondrial DNA control region (CR; 595 bp of the 3''end and 74 bp of flanking tRNA) and the ATP6 gene (630 bp fragment) were sequenced for 20 individuals (five from each locality). In addition, all individuals were genotyped with 12 microsatellite loci. The diversity and structure of the populations as well as the recent and ancient population declines were studied using specialized software.

Results

We detected three new haplotypes in the mtDNA CR and four haplotypes in the ATP6 gene of which three had not been described before. Previously, one CR haplotype and two ATP6 gene haplotypes had been identified as allochthonous, originating from Slovenia. Reconstruction of phylogenetic relations placed the remaining two CR haplotypes from the River Danube drainage of Serbia into a new clade, which is related to the previously described sister Slovenian clade. These two clades form a new Balkan clade. Microsatellite marker analysis showed that all four populations are genetically distinct from each other without any sign of intra-population structure, although stocking of the most diverse population (Drina River) was confirmed by mtDNA analysis. Recent and historical population declines of Serbian grayling do not differ from those of other European populations.

Conclusions

Our study shows that (1) the Ibar, Lim and Drina Rivers grayling populations are genetically distinct from populations outside of Serbia and thus should be managed as native populations in spite of some introgression in the Drina River population and (2) the Rzav River population is not appropriate for further stocking activities since it originates from stocked Slovenian grayling. However, the Rzav River population does not represent an immediate danger to other populations because it is physically isolated from these.     

Effects of a low-intensity electromagnetic field on fibroblast migration and proliferation

The aim of this study was to test if an extremely weak 1?GHz electromagnetic field (EMF), known to be in resonance with clusters of water molecules, has biological effects on human fibroblasts. We demonstrated that in an in vitro model of wound healing, this EMF can activate fibroblast migration. [(3)H]thymidine incorporation experiments demonstrated that the EMF could also activate fibroblast proliferation. Activation of the expression of human fibroblast growth factor 1 (HFGF1) after EMF exposure showed that molecular wound healing pathways are activated in response to this water-resonant EMF.     

Electrical signaling and photosynthesis: Can they co-exist together?

Mechanical irritation of trigger hairs and subsequent generation of action potentials have significant impact on photosynthesis and respiration in carnivorous Venus flytrap (Dionaea muscipula). Action potential-mediated inhibition of photosynthesis and stimulation of respiration is confined only to the trap and was not recorded in adjacent photosynthetic lamina. We showed that the main primary target of electrical signals on assimilation is in the dark enzymatic reaction of photosynthesis. Without doubt, the electrical signaling is costly, and the possible co-existence of such type of signals and photosynthesis in plant cell is discussed.Key words: action potential, carnivorous plant, Dionaea muscipula, electrical signaling, photosynthesis, respiration, Venus flytrapTrap closure of the Venus flytrap (Dionaea muscipula) is one of the fastest movements in plant kingdom. Mechanical irritation of trigger hairs protruding from upper leaf epidermis results in generation of action potential. At room temperature, two touches generate two action potentials and activate the trap snap shut in a fraction of second.¹ After the rapid movement secures the prey, struggling results in generation of further action potentials which cease to occur when the prey stops moving.² We documented that trigger hair irritation and subsequent generation of action potentials have significant effect on photosynthesis and respiration. Action potentials propagate in the trap and were not recorded in adjacent lamina (Fig. 1). This is in accordance with the observation that no changes of photosynthetic and respiration rate as well as effective quantum yield of photosystem II photochemistry were recorded in lamina. Detailed analysis of chlorophyll fluorescence kinetics revealed that the main primary target of action potentials is in the dark enzymatic reaction of photosynthesis and changes in quantum yield of primary photochemistry are just a consequence of decreased CO₂ fixation. However, electrical signals have probably also small effect on excitation energy trapping, charge stabilization and recombination reaction in photosystem II as measurements of fast chlorophyll a fluorescence transient indicates. This effect may be explained by repulsion of charges in reaction center of photosystem II.^3,4 The changes of photosynthesis upon impact of electrical signals probably have no benefit for plant and are only a negative consequences caused by the changes of the ionic environment.Open in a separate windowFigure 1Dionaea muscipula with entrapped wasp of the genus Polistes. Action potentials and rate of net assimilation at irradiance 80 µmol m⁻²s⁻ PAR (A_n) in response to 15 s mechanical trigger hair irritation (between 160–175 s) in trap (upper row) and photosynthetic lamina (lower row).These findings may have more consequences for plants in general. The electrical activity of plant cell was for the first time described by Burdon-Sanderson in 1873.⁵ Hence electrical signals do not belong exclusively to animal kingdom however they never develop the same degree of complexity as in animal nerves. Electrical signals are capable of transmitting signals more quickly over long distances when compared with chemical signals (e.g., hormones).^6,7 They are not confined only to the sensitive plants (e.g., Mimosa, Dionaea), but play also an important role in every non-sensitive plants and in both groups have significant effect on photosynthesis and respiration.^8–14 It is not surprising, that if electrical signals are costly in term of consumption of ATP and increased respiration with concurrent inhibition of photosynthesis, the same degree of complexity as in animals could not be developed. If plant growth depends on photosynthesis, this raises the question whether electrical signals and photosynthesis may co-exist together. The continuous electrical activity would inhibit the main source of energy for plants—photosynthetic assimilation. This may also explain why the plants are sessile organisms. For rapid coordinated movements, electrical activity plays an important role in animals. Unlike animals, plants usually rely on slow movements in which the role of plant hormones is indispensable. In this concept, it is not surprising that the more complex electrical activity was recorded in root transition zone—the heterotrophic part of plant body.^15,16 And this may also explain why the more evident electrical activity in the plant world has evolved in the traps of carnivorous plants like Dionaea, Aldrovanda or Drosera.^17–19 In general the traps of carnivorous plants are considered to be less efficient in photosynthesis.²⁰ Any of the action potentials produced by Drosera tentacles or Dionaea trap do not spread to photosynthetic active lamina, thus the main side of CO₂ fixation is protected.²¹ It is possible that such temporal carbon costs associated with insect trapping and retention may be outweighed by the benefits gained later from the prey—increased nitrogen concentration in the leaves stimulates photosynthetic assimilation.²² The possible ecophysiological impact of electrical signals on daily carbon gain in sensitive plants remains to be elucidated. We still do not completely understand the electrical signals in plants, and further research in this area is necessary to understand the full meaning of electrical activity in plants.     

Macromolecular docking restrained by a small angle X-ray scattering profile

While many structures of single protein components are becoming available, structural characterization of their complexes remains challenging. Methods for modeling assembly structures from individual components frequently suffer from large errors, due to protein flexibility and inaccurate scoring functions. However, when additional information is available, it may be possible to reduce the errors and compute near-native complex structures. One such type of information is a small angle X-ray scattering (SAXS) profile that can be collected in a high-throughput fashion from a small amount of sample in solution. Here, we present an efficient method for protein–protein docking with a SAXS profile (FoXSDock): generation of complex models by rigid global docking with PatchDock, filtering of the models based on the SAXS profile, clustering of the models, and refining the interface by flexible docking with FireDock. FoXSDock is benchmarked on 124 protein complexes with simulated SAXS profiles, as well as on 6 complexes with experimentally determined SAXS profiles. When induced fit is less than 1.5 Å interface C_α RMSD and the fraction residues of missing from the component structures is less than 3%, FoXSDock can find a model close to the native structure within the top 10 predictions in 77% of the cases; in comparison, docking alone succeeds in only 34% of the cases. Thus, the integrative approach significantly improves on molecular docking alone. The improvement arises from an increased resolution of rigid docking sampling and more accurate scoring.     

A systematic RNAi synthetic interaction screen reveals a link between p53 and snoRNP assembly

TP53 (tumour protein 53) is one of the most frequently mutated genes in human cancer and its role during cellular transformation has been studied extensively. However, the homeostatic functions of p53 are less well understood. Here, we explore the molecular dependency network of TP53 through an RNAi-mediated synthetic interaction screen employing two HCT116 isogenic cell lines and a genome-scale endoribonuclease-prepared short interfering RNA library. We identify a variety of TP53 synthetic interactions unmasking the complex connections of p53 to cellular physiology and growth control. Molecular dissection of the TP53 synthetic interaction with UNRIP indicates an enhanced dependency of TP53-negative cells on small nucleolar ribonucleoprotein (snoRNP) assembly. This dependency is mediated by the snoRNP chaperone gene NOLC1 (also known as NOPP140), which we identify as a physiological p53 target gene. This unanticipated function of TP53 in snoRNP assembly highlights the potential of RNAi-mediated synthetic interaction screens to dissect molecular pathways of tumour suppressor genes.     

Omeprazole inhibits proliferation and modulates autophagy in pancreatic cancer cells

Background

Omeprazole has recently been described as a modulator of tumour chemoresistance, although its underlying molecular mechanisms remain controversial. Since pancreatic tumours are highly chemoresistant, a logical step would be to investigate the pharmacodynamic, morphological and biochemical effects of omeprazole on pancreatic cancer cell lines.

Methodology/Principal Findings

Dose-effect curves of omeprazole, pantoprazole, gemcitabine, 5-fluorouracil and the combinations of omeprazole and 5-fluorouracil or gemcitabine were generated for the pancreatic cancer cell lines MiaPaCa-2, ASPC-1, Colo357, PancTu-1, Panc1 and Panc89. They revealed that omeprazole inhibited proliferation at probably non-toxic concentrations and reversed the hormesis phenomena of 5-fluorouracil. Electron microscopy showed that omeprazole led to accumulation of phagophores and early autophagosomes in ASPC-1 and MiaPaCa-2 cells. Signal changes indicating inhibited proliferation and programmed cell death were found by proton NMR spectroscopy of both cell lines when treated with omeprazole which was identified intracellularly. Omeprazole modulates the lysosomal transport pathway as shown by Western blot analysis of the expression of LAMP-1, Cathepsin-D and β-COP in lysosome- and Golgi complex containing cell fractions. Acridine orange staining revealed that the pump function of the vATPase was not specifically inhibited by omeprazole. Gene expression of the autophagy-related LC3 gene as well as of Bad, Mdr-1, Atg12 and the vATPase was analysed after treatment of cells with 5-fluorouracil and omeprazole and confirmed the above mentioned results.

Conclusions

We hypothesise that omeprazole interacts with the regulatory functions of the vATPase without inhibiting its pump function. A modulation of the lysosomal transport pathway and autophagy is caused in pancreatic cancer cells leading to programmed cell death. This may circumvent common resistance mechanisms of pancreatic cancer. Since omeprazole use has already been established in clinical practice these results could lead to new clinical applications.     

Dynamics of responses in compatible potato-Potato virus Y interaction are modulated by salicylic acid

To investigate the dynamics of the potato-Potato virus Y (PVY) compatible interaction in relation to salicylic acid-controlled pathways we performed experiments using non-transgenic potato cv. Désirée, transgenic NahG-Désirée, cv. Igor and PVY(NTN), the most aggressive strain of PVY. The importance of salicylic acid in viral multiplication and symptom development was confirmed by pronounced symptom development in NahG-Désirée, depleted in salicylic acid, and reversion of the effect after spraying with 2,6-dichloroisonicotinic acid (a salicylic acid-analogue). We have employed quantitative PCR for monitoring virus multiplication, as well as plant responses through expression of selected marker genes of photosynthetic activity, carbohydrate metabolism and the defence response. Viral multiplication was the slowest in inoculated potato of cv. Désirée, the only asymptomatic genotype in the study. The intensity of defence-related gene expression was much stronger in both sensitive genotypes (NahG-Désirée and cv. Igor) at the site of inoculation than in asymptomatic plants (cv. Désirée). Photosynthesis and carbohydrate metabolism gene expression differed between the symptomatic and asymptomatic phenotypes. The differential gene expression pattern of the two sensitive genotypes indicates that the outcome of the interaction does not rely simply on one regulatory component, but similar phenotypical features can result from distinct responses at the molecular level.     

Effect of hydrophobic mutations in the H2-H3 subdomain of prion protein on stability and conversion in vitro and in vivo

Prion diseases are fatal neurodegenerative diseases, which can be acquired, sporadic or genetic, the latter being linked to mutations in the gene encoding prion protein. We have recently described the importance of subdomain separation in the conversion of prion protein (PrP). The goal of the present study was to investigate the effect of increasing the hydrophobic interactions within the H2-H3 subdomain on PrP conversion. Three hydrophobic mutations were introduced into PrP. The mutation V209I associated with human prion disease did not alter protein stability or in vitro fibrillization propensity of PrP. The designed mutations V175I and T187I on the other hand increased protein thermal stability. V175I mutant fibrillized faster than wild-type PrP. Conversion delay of T187I was slightly longer, but fluorescence intensity of amyloid specific dye thioflavin T was significantly higher. Surprisingly, cells expressing V209I variant exhibited inefficient proteinase K resistant PrP formation upon infection with 22L strain, which is in contrast to cell lines expressing wild-type, V175I and T187I mPrPs. In agreement with increased ThT fluorescence at the plateau T187I expressing cell lines accumulated an increased amount of the proteinase K-resistant prion protein. We showed that T187I induces formation of thin fibrils, which are absent from other samples. We propose that larger solvent accessibility of I187 in comparison to wild-type and other mutants may interfere with lateral annealing of filaments and may be the underlying reason for increased conversion efficiency.     

Thermoregulatory responses to lipopolysaccharide in the mouse: dependence on the dose and ambient temperature

Most published studies of thermoregulatory responses of mice to LPS involved a stressful injection of LPS, were run at a poorly controlled and often subneutral ambient temperature (T(a)), and paid little attention to the dependence of the response on the LPS dose. These pitfalls have been overcome in the present study. Male C57BL/6 mice implanted with jugular vein catheters were kept in an environmental chamber at a tightly controlled T(a). The relationship between the T(a)s used and the thermoneutral zone of the mice was verified by measuring tail skin temperature, either by infrared thermography or thermocouple thermometry. Escherichia coli LPS in a wide dose range (10(0)-10(4) microg/kg) was administered through an extension of the jugular catheter from outside the chamber. The responses observed were dose dependent. At a neutral T(a), low (just suprathreshold) doses of LPS (10(0)-10(1) microg/kg) caused a monophasic fever. To a slightly higher dose (10(1.5) microg/kg), the mice responded with a biphasic fever. To even higher doses (10(1.75)-10(4) microg/kg), they responded with a polyphasic fever, of which three distinct phases were identified. The dose dependence and dynamics of LPS fever in the mouse appeared to be remarkably similar to those seen in the rat. However, the thermoregulatory response of mice to LPS in a subthermoneutral environment is remarkably different from that of rats. Although very high doses of LPS (10(4) microg/kg) did cause a late (latency, approximately 3 h) hypothermic response in mice, the typical early (latency, 10-30 min) hypothermic response seen in rats did not occur. The present investigation identifies experimental conditions to study LPS-induced mono-, bi-, and polyphasic fevers and late hypothermia in mice and provides detailed characteristics of these responses.     

Proinflammatory factors in saliva as possible markers for periodontal disease

Studies have indicated that host inflammatory proteins, enzymes and indicators of bone metabolism present in saliva differ in different types of periodontal disease. However, the number of markers analyzed was limited and the effect of edentulousness was not examined. We measured the concentration of host inflammatory proteins: C-reactive protein (CRP), C3 and C4 complement components, alpha-2-macroglobulin (alpha-2M) and tumor-necrosis factor (TNF) in unstimulated saliva of 14 periodontally healthy (PH), 9 edentulous persons (EP), 10 patients with chronic periodontitis (CP) and 18 with aggressive periodontitis (AgP). TNF was below the level of detection in all samples except one. Edentulous persons and patients with CP had significantly reduced concentrations of CRP, C3 and alpha-2M. Edentulous persons and AgP patients had lower C4 concentrations. We can conclude that edentulous persons and CP patients have reduced salivary concentrations of host inflammatory proteins. These findings suggest that a reduction in host responsiveness might play a role in the pathogenesis of CP.