Quantitative characterization of binding of small molecules to extracellular matrix

Extracellular matrix (ECM) is a major tissue component that, besides its cell support function, is implicated in cell-cell signaling, wound repair, cell adhesion, and other cell and tissue functions. For small molecules acting in tissues, including chemicals, signaling peptides, effectors, inhibitors, and other man-made and physiological compounds, non-specific binding to ECM is a critical phenomenon affecting their disposition. We describe here a method for a quantitative characterization of the ECM binding, using a solidified ECM layer incubated with medium containing studied small molecules. Working conditions of Matrigel, a commercial basement membrane preparation, were optimized in terms of the protein concentration, surface area, gel layer thickness, solidification time, and mixing speed. The release of proteins from the solidified layer into the buffer was monitored and taken into account. Two major proteins, laminin and collagen IV, dissolve at different rates. The Matrigel stability data, obtained under varying incubation conditions and gentle mixing, can also be useful in other ECM-related research. The experimental binding data, averaged over all binding sites, were analyzed assuming a fast linear binding. The binding constants were determined for 10 small organic molecules for both dissolved proteins and the solidified layer. The binding constants tend to increase with lipophilicity of the compounds, as characterized by the 1-octanol/water partition coefficients.     

The Expression and Diversity of Catalases in Isolates of Genus Comamonas in Response to the Oxidative Stress of a Polluted Environment

We have evaluated the role of monofunctional heme-containing catalase encoded by cat-1 gene from the soil bacterium Comamonas terrigena N3H in the response to various forms of oxidative stress. Our results indicate that this constitutively expressed catalase represents the major source for the defence of Comamonas terrigena cells against toxic peroxides but the cells can express also a second form of catalase that is bigger and its regulation is probably more complicated. The sequence analysis confirmed the presence of highly conserved catalase sequence motifs in two environmental strains of Comamonas terrigena but in those strains that were not exposed to oxidative stress, no such sequence motif could be detected. The results obtained underline the importance of catalase expression in the defence mechanism against oxidative stress in bacterial cells.     

The relationship between micronuclei in human lymphocytes and selected micronutrients in vegetarians and non-vegetarians

A vegetarian diet results in higher intake of vitamins and micronutrients, which - although providing antioxidant defence - may lead to deficiency in other micronutrients involved in DNA metabolism and stability (such as vitamins belonging to the B group). The principal difference among various vegetarian diets is the extent to which animal products are avoided. We have performed a pilot study to determine the relationship between the micronucleus frequency in lymphocytes and diet, and we compared the levels of Vitamins C and E, beta-carotene, B(12), folic acid, homocysteine and total antioxidant capacity in healthy vegetarians and non-vegetarians. The vegetarian group, consisting of 24 volunteers (13 women and 11 men), were matched for age and sex with 24 volunteers (12 women and 12 men) with a traditional dietary habit. Among the vegetarians were 13 lacto-ovo-vegetarians with average duration of vegetarian diet 10.8 years (ranging from 5 to 26 years) and 11 lacto-vegetarians with average duration of vegetarian diet 8.2 years (ranging from 3 to 15 years). Homocysteine, Vitamins C and E and beta-carotene levels in plasma were assayed by HPLC, and serum folate and Vitamin B(12) were determined with Elecsys Immunoassay tests. The total antioxidant capacity of plasma was estimated by measuring the ferric-reducing activity in a spectrophotometric assay. Micronuclei were measured in cytokinesis-blocked lymphocytes. Vegetarians had significantly higher levels of Vitamin C and beta-carotene (but not Vitamin E) in plasma compared with non-vegetarians (P<0.001). There were no significant differences in serum levels of folic acid and Vitamin B(12) between the monitored groups. Levels of folic acid in vegetarians correlated with length of vegetarianism (r=0.62, P=0.001, N=24). Vegetarians had elevated levels of homocysteine compared with non-vegetarians (P=0.007), as did vegetarian women compared with non-vegetarian women (P=0.031). We did not find any differences in total antioxidant capacity or in micronucleus frequency between the groups. Micronuclei correlated with age (r=0.62, P<0.001, N=48), women having higher frequencies than men. Multifactorial regression analysis showed significant effects of age, sex and total antioxidant capacity on micronucleus frequency (N=48, P<0.001).     

The vegetation of metalliferous and non-metalliferous grasslands in two former mine regions in Central Slovakia

We investigated the composition of the vegetation in two former mining regions in Central Slovakia: Banská Štiavnica with predominant Pb-Zn contamination and Staré Hory with a very high Cu content in the soil. Old heaps rich in heavy metals are covered with specific vegetation. On the Cu-rich spoil heaps, species-poor plant communities with prevailing Agrostis stolonifera, Avenella flexuosa, Acetosella vulgaris, Arabidopsis arenosa, Silene dioica, and S. vulgaris occur. Species such as Agrostis capillaris, Acetosella vulgaris, Arabidopsis arenosa, and Thlaspi caerulescens appear frequently on Pb-Zn mine wastes. Several differences in the vegetation structure were detected between the Pb-Zn and Cu mine heaps; higher amounts of vascular plants and fewer lichen species covered the Pb-Zn mine heaps. For the Cu mine heaps, on the contrary a small number of vascular species but a high number and coverage of lichen species, especially Ceratodon purpureus and Cladonia arbuscula subsp. mitis were typical. The non-metalliferous meadows in the vicinity of the mines showed uniform structure but a higher species diversity.     

An Effective Combination of Two Different Methods of Postconditioning

Ischemic tolerance based on the synthesis of protective proteins acquires its full strength by repeated exposure to stress, and "the end effector of tolerance" may paradoxically be activated by the second or lethal stress, particularly in the case of preconditioning. That happens when an additional nonspecific stressor is applied either before (preconditioning) or after (postconditioning) the period of lethal ischemia. A combination of antioxidants with pre or postconditioning prevents the acquisition of tolerance, and in the case of more severe attacks repeated stress can lead to accumulation of damage. Our attempt to weaken ischemic injury to hippocampal CA1 with antioxidants applied after lethal stress, i.e. before delayed postconditioning, was ineffective. We then tried using rapid postconditioning consisting of 30-s reperfusion alternating with 15-s ischemia repeated three times and applied immediately at the end of lethal ischemia as a tool decreasing post-ischemic production of reactive oxygen species, and combining that with delayed postconditioning consisting of an i.p. injection of Bradykinin 2?days after lethal ischemia. This approach once more confirmed the efficacy of both rapid as well as delayed postconditioning but, more importantly, it demonstrated the possibility of effectively combining these two procedures. Our findings further confirm that in cases of delayed neuronal death, which is practically pathologically-induced apoptosis, there exists a 2-day-wide therapeutic window that can be effectively exploited.     

Bisprimer--a program for the design of primers for bisulfite-based genomic sequencing of both plant and Mammalian DNA samples

Plants and animals differ in the sequence context of the methylated sites in DNA. Plants exhibit cytosine methylation in CG, CHG, and CHH sites, whereas CG methylation is the only form present in mammals (with an exception of the early embryonic development). This fact must be taken into account in the design of primers for bisulfite-based genomic sequencing because CHG and CHH sites can remain unmodified. Surprisingly, no user-friendly primer design program is publicly available that could be used to design primers in plants and to simultaneously check the properties of primers such as the potential for primer-dimer formation. For studies concentrating on particular DNA loci, the correct design of primers is crucial. The program, called BisPrimer, includes 2 different subprograms for the primer design, the first one for mammals and the second one for angiosperm plants. Each subprogram is divided into 2 variants. The first variant serves to design primers that preferentially bind to the bisulfite-modified primer-binding sites (C to U conversion). This type of primer preferentially amplifies the bisulfite-converted DNA strands. This feature can help to avoid problems connected with an incomplete bisulfite modification that can sometimes occur for technical reasons. The second variant is intended for the analysis of samples that are supposed to consist of a mixture of DNA molecules that have different levels of cytosine methylation (e.g., pollen DNA). In this case, the aim is to minimize the selection in favor of either less methylated or more methylated molecules.     

Effects of density on growth rates of four benthic diatoms and variations in biochemical composition associated with growth phase

Diatom cell quantity and their biochemical composition vary among species and are greatly affected by harvest stage or culture conditions. This study compares growth pattern, cell attachment, and biochemical composition of four diatoms suitable for abalone post-larvae: Navicula incerta, Proschkinia sp., Nitzschia sp., and Amphora sp. The four diatoms were grown in F/2 medium at 28.5?±?1.4°C, under 62?±?8?μmol?photons?m^?2?s^?1, at different original inoculating densities (0.05?×?10⁶, 0.10?×?10⁶, and 0.25?×?10⁶?cells?mL^?1) and were harvested in log and stationary phase of growth for biochemical analysis. Total protein, carbohydrate, lipid, and ash composition, as well as fatty acid composition, were determined. All diatoms grew better when inoculated at 0.10?×?10⁶?cell?mL^?1 with Proschkinia sp. reaching the highest cell density of 6.56?×?10⁶?cells?mL^?1 in log phase. Amphora sp. had the highest cell attachment capacity when inoculated at 0.10?×?10⁶?cell?mL^?1 (11,580?cells?mm^?2), whereas N. incerta had the lowest (7,750?cells?mm^?2). Protein and lipid (percent dry weight) contents were generally highest in cells during log phase of growth; Amphora sp. in log phase of growth had the highest lipid content of 9.74% DW, whereas significant differences in carbohydrate between the two growth phases were only observed for Proschkinia sp. Besides, all diatoms had higher energy contents in log phase of growth. There were no significant differences in ash content among the four diatoms. Polyunsaturated fatty acid (PUFA) content ranged from 23.25% to 38.62% of the total fatty acids, and the four diatoms tested were richer in n-3 PUFA than in n-6 PUFA. All the diatoms had significant quantities of 20:5n-3 (EPA) (between 12.69% and 17.68% of TFA), and Proschkinia sp., in log phase of growth, had the highest quantity of arachidonic acid (20:4n-6; ARA). The results highlight the influence of culture conditions and harvest protocols on diatom nutritive value and enabled a preliminary approach towards the selection of novel diatom species.     

Maternal Separation Induced Alterations of Neurogenesis in the Rat Rostral Migratory Stream

1. The aim of our study was to investigate the possibility that maternal separation, an experimental model for studies of early environmental influences, has an effect on postnatal neurogenesis in neurogenic pathway—the rostral migratory stream (RMS). 2. Rat pups were subjected to maternal separation daily for 3 h, starting from the first postnatal day (P1) till P14 or P21. In the first two groups, brains were analyzed at the age of P14 and P21, respectively. In the third group, after 3 weeks of maternal separation, 1 week of normal rearing was allowed, and the brains were analyzed at P28. The controls matched the age of maternally separated animals. Dividing cells were labeled by bromodeoxyuridine; dying cells were visualized by Fluoro-Jade C and nitric oxide (NO) producing cells by NADPH-diaphorase histochemistry. 3. Quantitative analysis of proliferating cells in the RMS showed that maternal separation decreased the number of dividing cells in all experimental groups. This decrease was most prominent in the caudal part of the RMS. The amount of dying cells was increased at the end of 3 weeks of maternal separation as well as 1 week later. The number of differentiated nitrergic cells in the RMS was increased at the end of 2 or 3 weeks of maternal separation, respectively. Besides quantitative changes, maternally separated animals showed an accelerated maturation of nitrergic cells. 4. Our results indicate that an exposure of rats to adverse environmental factors in early postnatal periods may induce acute site-specific changes in the RMS neurogenesis.