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.     

Head and neck squamous cancer stromal fibroblasts produce growth factors influencing phenotype of normal human keratinocytes

Epithelial–mesenchymal interaction between stromal fibroblasts and cancer cells influences the functional properties of tumor epithelium, including the tumor progression and spread. We compared fibroblasts prepared from stroma of squamous cell carcinoma and normal dermal fibroblasts concerning their biological activity toward normal keratinocytes assessed by immunocytochemistry and profiling of gene activation for growth factors/cytokines by microarray chip technology. IGF-2 and BMP-4 were determined as candidate factors responsible for tumor-associated fibroblast activity that influences normal epithelia. This effect was confirmed by addition of recombinant IGF-2 and BMP4, respectively, to the culture medium. This hypothesis was also verified by inhibition experiments where blocking antibodies were employed in the medium conditioned by cancer-associated fibroblast. Presence of these growth factors was also detected in tumor samples.     

The effect of Stratiotes aloides L. and nutrients on the growth rate of Lemna minor L.

We tried to find the reasons for frequently observed low biomass of Lemna minor among floating rosettes of Stratiotes aloides as opposed to the abundance of Spirodela polyrhiza in these stands. The effect of S. aloides on L. minor was analysed in outdoor culture experiments. The duckweed collected from among dense stands of the floating form of S. aloides (test sites) showed a significantly lower growth rate than that from stands free of the water soldier (control sites). Water from the latter stands was significantly richer in nitrate-nitrogen and ammonium-nitrogen, but not in soluble reactive phosphorus suggesting possible nutrient depletion as a reason for observed differences. Growth rates of L. minor were indeed significantly correlated with in situ concentrations of all dissolved nutrients and showed saturation at around 0.18 mg N-NH₄ dm⁻³ and 0.05 mg SRP dm⁻³ above which the growth rates did not increase significantly. We used stepwise regression to test the combined effect of nutrients and the presence/absence of S. aloides on the growth rate of L. minor. The regression showed a negligible effect of ammonium ions and nitrates on the growth rate of the duckweed. At low concentrations of soluble reactive phosphorus the presence of both the S. aloides and SRP concentrations significantly affected the growth of L. minor. Above saturating SRP concentrations none of the two effects was significant. Results of our experiments seem to suggest that the presence of S. aloides exerts a negative effect on the growth of L. minor only at low concentrations of soluble phosphorus. Since the depletion of nutrients in water by the floating form of S. aloides is unlikely, we point to S. polyrhiza as a superior competitor for nutrients and suggest a possible allelopathic effect of the water soldier on L. minor.     

Non-native fish species in Slovak waters: origins and present status

Freshwater fishes recorded in the territory of Slovakia include 95 fish species. As many as one third of these are allochthonous fish species belonging to 14 families, among which several have not occurred in Slovakia recently. Historically, there were three main periods of introduction: the first is the beginning of the 20^th century, the second includes two decades between 1955 and 1975 and the third period is from the year 1990 up to the present time. The origins of the exotic species seen in Slovakia are the four continents — Africa (3), North America (7), Central America (3), and Asia (13) and ten of them are from different regions in Europe. The purpose of intentional introductions of non-native species was to occupy vacant ecological niches in the ecosystems reshaped by human activities, fish stocking, angling or fish farming. Some of these species spread from their original ranges or they penetrated spontaneously from the adjacent countries via the river network system. At the present time, 76 fish species in total form populations in Slovakia. There are 54 autochthonous and 22 allochthonous species, 14 of them are exotic fishes. The invasive characters in 13 fish species were considered, the recent native/total fish ratio is 0.71.     

Intensive physical activity increases peripheral blood dendritic cells

We analyzed the frequency and absolute numbers of circulating myeloid and plasmacytoid DCs in peripheral blood and evaluated their maturation status to test the hypothesis that significant physical stress to the body might induce measurable changes in DCs subsets, phenotype and function, which would complete existing knowledge about the response of the cellular immune system to an acute exercise in top sportsmen. We evaluated the heart rate and draw blood samples before and after the physical load in 18 profesional ice-hockey players. We observed an increase in leukocytes numbers with a predominant increase in the population of DCs and lymphocytes after exercise. Both myeloid and plasmacytoid DCs increased significantly. We found a correlation between the increase of peripheral blood DCs and serum epinephrine and norepinephrine levels. Increase in peripheral blood DCs also correlates with the extent of heart rate elevation during exercise.     

The Indispensable N-Terminal Half of eIF3j/HCR1 Cooperates with its Structurally Conserved Binding Partner eIF3b/PRT1-RRM and with eIF1A in Stringent AUG Selection

Despite recent progress in our understanding of the numerous functions of individual subunits of eukaryotic translation initiation factor (eIF) 3, little is known on the molecular level. Using NMR spectroscopy, we determined the first solution structure of an interaction between eIF3 subunits. We revealed that a conserved tryptophan residue in the human eIF3j N-terminal acidic motif (NTA) is held in the helix α1 and loop 5 hydrophobic pocket of the human eIF3b RNA recognition motif (RRM). Mutating the corresponding “pocket” residues in its yeast orthologue reduces cellular growth rate, eliminates eIF3j/HCR1 association with eIF3b/PRT1 in vitro and in vivo, affects 40S occupancy of eIF3, and produces a leaky scanning defect indicative of a deregulation of the AUG selection process. Unexpectedly, we found that the N-terminal half of eIF3j/HCR1 containing the NTA is indispensable and sufficient for wild-type growth of yeast cells. Furthermore, we demonstrate that deletion of either j/HCR1 or its N-terminal half only, or mutation of the key tryptophan residues results in the severe leaky scanning phenotype partially suppressible by overexpressed eIF1A, which is thought to stabilize properly formed preinitiation complexes at the correct start codon. These findings indicate that eIF3j/HCR1 remains associated with the scanning preinitiation complexes and does not dissociate from the small ribosomal subunit upon mRNA recruitment, as previously believed. Finally, we provide further support for earlier mapping of the ribosomal binding site for human eIF3j by identifying specific interactions of eIF3j/HCR1 with small ribosomal proteins RPS2 and RPS23 located in the vicinity of the mRNA entry channel. Taken together, we propose that eIF3j/HCR1 closely cooperates with the eIF3b/PRT1 RRM and eIF1A on the ribosome to ensure proper formation of the scanning-arrested conformation required for stringent AUG recognition.     

Cold acclimation of forage grasses in relation to pink snow mould (Microdochium nivale) resistance

The aim of our work is to investigate the changes in phenolic level, PAL activity and heat production rate induced during pre-hardening at 12°C and cold acclimation at 2°C of the forage grasses Festulolium, meadow fescue, tall fescue and Italian ryegrass in relation to their resistance to snow mould caused by Microdochium nivale. Meadow fescue and tall fescue were most resistant to M. nivale infection, while Italian ryegrass demonstrated the least resistance to this fungus inoculation. Festulolium, meadow fescue and tall fescue responded similarly to low temperature, while Italian ryegrass demonstrated considerable disturbance of energy balance and lower phenolic concentration, which could explain a higher susceptibility of the latter species to infection by M. nivale. The enhanced level of phenolic compounds, probably utilised for cell wall lignification as well as equilibrium of the metabolic activity observed in meadow fescue and tall fescue, is very important for both cold and pathogen-resistance mechanisms. The studied Festulolium cultivar ‘Felopa’, a hybrid of the Lolium multiflorum and Festuca pratensis genomes, was characterised by changes in biochemical parameters similar to the resistant meadow fescue and tall fescue.     

Evaluation of diffusion and dilution methods to determine the antibacterial activity of plant extracts

The aim of this study was to evaluate diffusion and dilution methods for determining the antibacterial activity of plant extracts and their mixtures. Several methods for measurement of the minimal inhibitory concentration (MIC) of a plant extract are available, but there is no standard procedure as there is for antibiotics. We tested different plant extracts, their mixtures and phenolic acids on selected gram-positive (Staphylococcus aureus, Bacillus cereus, and Listeria monocytogenes) and gram-negative bacteria (Escherichia coli O157:H7, Salmonella Infantis, Campylobacter jejuni, Campylobacter coli) with the disk diffusion, agar dilution, broth microdilution and macrodilution methods. The disk diffusion method was appropriate only as a preliminary screening test prior to quantitative MIC determination with dilution methods. A comparison of the results for MIC obtained by agar dilution and broth microdilution was possible only for gram-positive bacteria, and indicated the latter as the most accurate way of assessing the antimicrobial effect. The microdilution method with TTC (2,3,5-triphenyl tetrazolium chloride) or INT (2-p-iodophenyl-3-p-nitrophenyl-5-phenyl tetrazolium chloride) to indicate the viability of aerobic bacteria was found to be the best alternative approach, while only ATP determination was appropriate for microaerophilic Campylobacter spp. Using survival curves the kinetics of bacterial inactivation on plant extract exposure was followed for 24 h and in this way the MIC values determined by the microdilution method were confirmed as the concentrations of extracts that inhibited bacterial growth. We suggest evaluation of the antibacterial activity of plant extracts using the broth microdilution method as a fast screening method for MIC determination and the macrodilution method at selected MIC values to confirm bacterial inactivation. Campylobacter spp. showed a similar sensitivity to plant extracts as the tested gram-positive bacteria, but S. Infantis and E. coli O157:H7 were more resistant.     

New aromatic monoesters of α-aminoaralkylphosphonic acids as inhibitors of aminopeptidase N/CD13

A series of new aromatic monoesters of α-aminoaralkylphosphonic acids were synthesized by selective hydrolysis of corresponding aromatic diesters of α-aminoaralkylphosphonic acids. New potential inhibitors of aminopeptidase N/CD13, an enzyme important in tumour angiogenesis, were developed. Some derivatives of the homophenylalanine and norleucine related monoaryl phosphonates displayed higher inhibition potency than corresponding α-aminoaralkylphosphonic acids toward aminopeptidase N/CD13. The effect of one of the new inhibitors on the growth of human PANC-1 and HT-1080 cell lines was examined, either alone or in combination with TNF-α.