Multi-proxy analysis of waterlogged preserved Late Neolithic canine excrements

Vegetation History and Archaeobotany - Multi-proxy analysis of the coprolites which were found during excavations at two Late Neolithic (fourth millennium bc) pile-dwelling sites (Črnelnik and...     

A Model of Piezo1-Based Regulation of Red Blood Cell Volume

A red blood cell (RBC) performs its function of adequately carrying respiratory gases in blood by its volume being ～60% of that of a sphere with the same membrane area. For this purpose, human and most other vertebrate RBCs regulate their content of potassium (K⁺) and sodium (Na⁺) ions. The focus considered here is on K⁺ efflux through calcium-ion (Ca²⁺)-activated Gárdos channels. These channels open under conditions that allow Ca²⁺ to enter RBCs through Piezo1 mechanosensitive cation-permeable channels. It is postulated that the fraction of open Piezo1 channels depends on the RBC shape as a result of the curvature-dependent Piezo1-bilayer membrane interaction. The consequences of this postulate are studied by introducing a simple model of RBC osmotic behavior supplemented by the dependence of RBC membrane K⁺ permeability on the reduced volume (i.e., the ratio of cell volume to its maximal possible volume) of RBC discoid shapes. It is assumed that because of its intrinsic curvature and strong interaction with the surrounding membrane, Piezo1 tends to concentrate in the dimple regions of these shapes, and the fraction of open Piezo1 channels depends on the membrane curvature in that region. It is shown that the properties of the described model can provide the basis for the formation of the negative feedback loop that interrelates cell volume and its content of potassium ions. The model predicts the relation, valid for each cell in an RBC population, between RBC volume and membrane area, thus explaining the large value of the measured membrane area versus the volume correlation coefficient. The mechanism proposed here for RBC volume regulation is in accord with the loss of this correlation in RBCs of Piezo1 knockout mice.     

Plant economy at a late Neolithic lake dwelling site in Slovenia at the time of the Alpine Iceman

We present the results of a plant macroremain study of the late Neolithic lakeshore settlement Stare gmajne (SG) at Ljubljansko barje, Slovenia, with cultural horizons that ended around 3330 and 3110 cal. b.c., as obtained by dendrochronological and radiocarbon dating of the most frequent construction timbers of Quercus sp. (oak) and Fraxinus sp. (ash). Fourteen systematically taken samples were investigated, using standard methods for studying waterlogged plant remains, which had been developed during lake dwelling research north of the Alps. Most of the remains were preserved in a waterlogged state, and we identified a total of 93 taxa. The most important cultivated plants were Triticum dicoccum (emmer), Hordeum vulgare (six-rowed naked barley), T. monococcum (einkorn), Linum usitatissimum (flax) and Papaver somniferum (opium poppy). The numerous possibly gathered plants also included Trapa natans (water chestnut) and Vitis vinifera ssp. sylvestris (wild grapevine). Chenopodium album (goosefoot) and Brassica rapa (turnip) with seeds/fruits rich in oil and starch were probably gathered as well. Comparisons of the Stare gmajne results with contemporary north Alpine sites (NA) showed, among other things, that Triticum durum/turgidum (tetraploid naked wheat), frequent at NA, was not found at SG. Trapa natans (water chestnut) was rare and Vitis (grapevine) was not found at NA. The observed differences in the wild plant spectra may have ecological causes, for example a warmer climate south of the Alps, but differences in cultivar spectra are more likely for cultural-historical reasons.     

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.     

Cereal chaff used as temper in loom-weights: new evidence from a Slovenian Eneolithic pile-dwelling site (ca. 3100 cal <Emphasis Type="SmallCaps">bc</Emphasis>)

We present new evidence of the intentional use of cereal by-products at Stare gmajne, an Eneolithic pile-dwelling site in Slovenia, dated approximately 3160–3100 cal bc. The chaff material, which had been used for tempering, was discovered inside one of the largest discovered loom-weights and analysed. Clay, which was used by the dwellers to make the weight, was tempered with cereal chaff to reinforce it. The practice of tempering, not necessarily for loom weights, has already been proven for earlier settlements, mostly in arid areas where firewood, grazing and building material were scarce. However, tempering has rarely been found in European prehistoric sites. More than 1,800 carbonised and half-carbonised, excellently preserved and well identifiable cereal plant macroremains in less than 1 l of waterlogged clayey material were sorted and counted. Among the recognized plant macroremains, barley rachis fragments and glume wheat (emmer and einkorn) by-products such as spikelet forks and glume bases prevailed. A few grains were also found. Cultivation of the main crops of emmer, einkorn and barley at Slovenian Eneolithic pile-dwelling sites was confirmed again. Among the chaff, a new “strange type” of Triticum dicoccum (emmer) spikelet forks was discovered. The size of the weight and the intentional local use of cereal by-products as temper suggest that late Neolithic (Eneolithic) pile-dwelling societies all around the Alps were highly organized and developed due to expansion of crop production and processing.     

Recovery techniques for waterlogged archaeological sediments: a comparison of different treatment methods for samples from Neolithic lake shore settlements

This paper presents the first comparable overview of different recovery techniques used for waterlogged Neolithic sediments in the surroundings of the Alps in the last decades. Such an investigation became necessary because it was not known which parts of plants and types of remains were absent or completely underrepresented due to inappropriate recovery techniques in Slovenian archaeobotany up to 2006. During the 2007 excavation of the approximately 5,200 years old Neolithic pile dwelling site of Stare gmajne, Ljubljansko barje, Slovenia, we compared three methods for the investigation of botanical macroremains: method 1 (M1) included rough wet-sieving and subsequent drying of the fractions; method 2 (M2) rough wet sieving and keeping the fractions wet; and method 3 (M3) washing over and keeping the fractions wet. M3 with gentle washing, systematic subsampling, examination, and sorting of macroremains while wet, as well as using 0.355 mm as the smallest sieve mesh size gave the best results. When using the cruder M2 or M1 methods, waterlogged uncarbonized seeds of taxa such as Linum usitatissimum, Papaver somniferum and Brassica rapa, waterlogged chaff of Cerealia and pericarps of Maloideae and Quercus sp., which are all fragile, were underrepresented or even completely absent and therefore the plant spectra were strongly biased. On the contrary, taxa with lignified seed/fruit walls like Cornus mas, Corylus avellana or Rubus sp. were overrepresented when using the M2 and particularly the M1 method. The application of the M3, instead of the M1 method which has been traditionally used in Slovenian archaeobotany, helped us to identify uncarbonized remains of Linum usitatissimum and various species of Triticum for the first time in a waterlogged Neolithic site in Slovenia. Our study should contribute to a standardization of methods, which is desperately needed in archaeobotany. The study clearly shows that the plant spectra can be strongly biased if inappropriate handling techniques are used. The conclusions hold for all kinds of waterlogged sediments of different periods.     

Vibrio sp. DSM 14379 Pigment Production—A Competitive Advantage in the Environment?

The ability to produce several antibacterial agents greatly increases the chance of producer’s survival. In this study, red-pigmented Vibrio sp. DSM 14379 and Bacillus sp., both isolated from the same sampling volume from estuarine waters of the Northern Adriatic Sea, were grown in a co-culture. The antibacterial activity of the red pigment extract was tested on Bacillus sp. in microtiter plates. The MIC₅₀ for Bacillus sp. was estimated to be around 10⁻⁵ mg/L. The extract prepared form the nonpigmented mutant of Vibrio sp. had no antibacterial effect. The pigment production of Vibrio sp. was studied under different physicochemical conditions. There was no pigment production at high or low temperatures, high or low salt concentrations in peptone yeast extract (PYE) medium, low glucose concentration in mineral growth medium or high glucose concentration in PYE medium. This indicates that the red pigment production is a luxurious good that Vibrio sp. makes only under favorable conditions. The Malthusian fitness of Bacillus sp. in a co-culture with Vibrio sp. under optimal environmental conditions dropped from 4.0 to −7.6, which corresponds to three orders of magnitude decrease in the number of CFU relative to the monoculture. The nonpigmented mutant of Vibrio sp. in a co-culture with Bacillus sp. had a significant antibacterial activity. This result shows that studying antibacterial properties in isolation (i.e. pigment extract only) may not reveal full antibacterial potential of the bacterial strain. The red pigment is a redundant antibacterial agent of Vibrio sp.     

Asymmetric Response of Carbon Metabolism at High and Low Salt Stress in <Emphasis Type="Italic">Vibrio</Emphasis> sp. DSM14379

Energy redistribution between growth and maintenance in salt-stressed cells is especially important for bacteria living in estuarine environments. In this study, Gram-negative bacterium Vibrio sp. DSM14379, isolated from the estuarine waters of the northern Adriatic Sea, was grown aerobically in a peptone–yeast extract medium with different salt concentrations (ranging from 0.3% to 10% (w/v) NaCl). Carbon flux through the central metabolic pathways was determined at low and high salt concentrations. At low salt concentrations, total endogenous respiration, dehydrogenase activity, and net intracellular adenosine triphosphate (ATP) concentration significantly increased, the phosphofructokinase and pyruvate kinase activity decreased, whereas glucose-6-phosphate dehydrogenase activity remained unchanged. The carrying capacity of bacterial culture decreased dramatically, indicating a severe metabolic imbalance at low salt concentrations. At high salt concentrations, carrying capacity decreased gradually. There was a large increase in glucose-6-phosphate dehydrogenase activity, which correlated with a 10-fold increase in concentration of osmoprotectant l-proline. There was no significant change of net intracellular ATP concentration, phosphofructokinase, or pyruvate kinase activity. The results indicate that Vibrio sp. DSM14379 central metabolic pathways respond to low and high salt concentrations asymmetrically; cells are better adapted to high salt concentrations. In addition, cells in the stationary phase can tolerate induced salt stress without a significant change in dehydrogenase activity or endogenous respiration for at least 1 h, but need to alter their macromolecular composition and carbon flux distribution for long-term survival.     

Signalling Network Construction for Modelling Plant Defence Response

Plant defence signalling response against various pathogens, including viruses, is a complex phenomenon. In resistant interaction a plant cell perceives the pathogen signal, transduces it within the cell and performs a reprogramming of the cell metabolism leading to the pathogen replication arrest. This work focuses on signalling pathways crucial for the plant defence response, i.e., the salicylic acid, jasmonic acid and ethylene signal transduction pathways, in the Arabidopsis thaliana model plant. The initial signalling network topology was constructed manually by defining the representation formalism, encoding the information from public databases and literature, and composing a pathway diagram. The manually constructed network structure consists of 175 components and 387 reactions. In order to complement the network topology with possibly missing relations, a new approach to automated information extraction from biological literature was developed. This approach, named Bio3graph, allows for automated extraction of biological relations from the literature, resulting in a set of (component1, reaction, component2) triplets and composing a graph structure which can be visualised, compared to the manually constructed topology and examined by the experts. Using a plant defence response vocabulary of components and reaction types, Bio3graph was applied to a set of 9,586 relevant full text articles, resulting in 137 newly detected reactions between the components. Finally, the manually constructed topology and the new reactions were merged to form a network structure consisting of 175 components and 524 reactions. The resulting pathway diagram of plant defence signalling represents a valuable source for further computational modelling and interpretation of omics data. The developed Bio3graph approach, implemented as an executable language processing and graph visualisation workflow, is publically available at http://ropot.ijs.si/bio3graph/and can be utilised for modelling other biological systems, given that an adequate vocabulary is provided.     

Jellyfish modulate bacterial dynamic and community structure

Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into possible changes in bacterial population dynamics and nutrient pathways following jellyfish blooms which have important implications for ecology of coastal waters.