Sampling issues in quantitative analysis of dendritic spines morphology

ABSTRACT: BACKGROUND: Quantitative analysis of changes in dendritic spine morphology has become an interesting issue in contemporary neuroscience. However, the diversity in dendritic spines population might seriously influence the results of measurements in which their morphology is studied, the detection of differences in spine morphology between control and test group is often compromised by the number of dendritic spines taken for analysis. In order to estimate how severe is such an impact we have performed Monte Carlo simulations examining various experimental setups and statistical approaches. The confocal images of dendritic spines from hippocampal dissociated cultures have been used to create a set of variables exploited as the simulation resources. RESULTS: The tabulated results of simulations are given, providing the number of dendritic spines required for the detection of hidden morphological differences between control and test group, in spine head-width, length and area. It turns out that this is the head-width among these three variables, where the changes are most easily detected. Simulation of changes occurring in a subpopulation of spines reveal the strong dependence of detectability on the statistical approach applied. The analysis based on comparison of percentage of spines in subclasses is less sensitive than the direct comparison of relevant variables describing spines morphology. CONCLUSIONS: We evaluated the sampling aspect and effect of systematic morphological variation on detecting the differences in spine morphology. Provided results may serve as a guideline in selecting the number of samples to be studied in a planned experiment. Our simulations might be a step towards the development of a standardized method of quantitative comparison of dendritic spines morphology, in which different sources of errors are considered.     

Bragg-Scattered Surface Plasmon Microscopy: Theoretical Study

We present a new approach to surface plasmon microscopy with high refractive index sensitivity and spatial resolution that is not limited by the propagation length of surface plasmons. It is based on a nanostructured metallic sensor surface supporting Bragg-scattered surface plasmons. We show that these non-propagating surface plasmon modes are excellently suited for spatially resolved observations of refractive index variations on the sensor surface owing to their highly confined field profile perpendicular to as well as parallel to the metal interface. The presented theoretical study reveals that this approach enables reaching similar refractive index sensitivity as regular surface plasmon resonance (SPR) microscopy and offers the advantage of improved spatial resolution when observing dielectric features with lateral size <10???m for the wavelength around 800?nm and gold as the SPR-active metal. This paper demonstrates the potential of Bragg-scattered surface plasmon microscopy for high-throughput SPR biosensing with high-density microarrays.     

Mortality of vertebrates on a road crossing the Biebrza Valley (NE Poland)

Mortality of vertebrates was monitored on a local road running across Poland’s Biebrza River Valley during 2 years (August 2005–July 2006). On the basis of distance from the river and surrounding habitats, the road (of total length 2,510 m) was divided into three stretches. The road was monitored on foot by two people every month, over a few consecutive days. A total of 1,892 road kills representing at least 47 species were found. Of these, 90.7% were amphibians, 4.2% mammals, 3.1% birds and 2.0% reptiles. Most (70%) of the amphibians were anurans, with the common toad, common frog and moor frog among them together accounting for 82% of the total. Mortality among amphibians differed between months, most anurans dying in May and August, while a majority of Urodela are lost in October. The peaks in mortality were connected with the migration of adult amphibians in spring and juveniles in summer and autumn. The number of amphibians killed was greatest on the (wettest) stretch adjacent to the river and decreased with distance from it. Mortality among birds was highest in July—probably in association with the dispersal of young individuals. Among recorded mammalian road kills, there was a prevalence of small rodents (mainly voles) and insectivores (mainly shrews). Medium-sized mammals were found only accidentally. Mortality in general was conditioned by the number of anurans killed.     

The release of soluble forms of TRAIL and DR5 by neutrophils of oral cavity cancer patients

In the present study we examined the release of the soluble form of TRAIL by neutrophils (PMN) derived from patients with oral cavity cancer. Simultaneously, we estimated the ability of PMNs of these patients to release the soluble form of DR5 receptor, a natural regulatory protein of TRAIL. The obtained results were confronted with the serum levels of sTRAIL and sDR5. The cells were isolated from 21 patients with squamous cell carcinoma of oral cavity at diagnosis and three weeks after surgery treatment. For comparative purposes we performed similar examinations in autologous peripheral blood mononuclear cells (PBMC). Cytoplasmic protein fractions of the cells were analyzed for the presence of TRAIL and DR5 by western blotting. Soluble TRAIL and soluble DR5 concentrations in the culture supernatants of cells were confronted with their serum levels using ELISA kit. PMN and PBMC of the whole cancer patient group expressed decreased TRAIL protein and unchanged expression of DR5 receptor in comparison with the control group. Unchanged release of sTRAIL by PMNs of patients in Stage II was accompanying the decrease of the ability of PBMC to secrete this protein. In patients in Stage IV the secretion of sTRAIL by PMNs and PBMC was impaired. In contrast to changes in sTRAIL secretion by PMN and PBMC of oral cavity cancer patients, the secretion of sDR5 by these cells was unchanged. The serum levels of sTRAIL were increased in patients in Stage II before treatment and decreased in the same patients after treatment. The altered ability of PMN of PBMC to secrete sTRAIL may have different implications for the immune response of patients with oral cavity cancer cells at different stages of disease.     

Effect of quinones on formation and properties of bacteriochlorophyll c aggregates

Chlorosomes of green photosynthetic bacterium Chlorobium tepidum contain aggregates of bacteriochlorophyll c (BChl c) with carotenoids and isoprenoid quinones. BChl aggregates with very similar optical properties can be prepared also in vitro either in non-polar solvents or in aqueous buffers with addition of lipids and/or carotenoids. In this work, we show that the aggregation of BChl c in aqueous buffer can be induced also by quinones (vitamin K₁ and K₂), provided they are non-polar due to a hydrophobic side-chain. Polar vitamin K_3, which possess the same functional group as K₁ and K₂, does not induce the aggregation. The results confirm a principal role of the hydrophobic interactions as a driving force for the aggregation of chlorosomal BChls. The chlorosomal quinones play an important role in a redox-dependent excitation quenching, which may protect the cells against damage under oxygenic conditions. We found that aggregates of BChl c with vitamin K₁ and K₂ exhibit an excitation quenching as well. The amplitude of the quenching depends on quinone concentration, as determined from fluorescence measurements. No lipid is necessary to induce the quenching, which therefore originates mainly from interactions of BChl c with quinones incorporated in the aggregate structure. In contrast, only a weak quenching was observed for dimers of BChl c in buffer (either with or without vitamin K₃) and also for BChl c aggregates prepared with a lipid (lecithin). Thus, the weak quenching seems to be a property of BChl c itself.     

ErbB-2 and met reciprocally regulate cellular signaling via plexin-B1

Sema4D-induced activation of plexin-B1 has been reported to evoke different and sometimes opposing cellular responses. The mechanisms underlying the versatility of plexin-B1-mediated effects are not clear. Plexin-B1 can associate with the receptor tyrosine kinases ErbB-2 and Met. Here we show that Sema4D-induced activation and inactivation of RhoA require ErbB-2 and Met, respectively. In breast carcinoma cells, Sema4D can have pro- and anti-migratory effects depending on the presence of ErbB-2 and Met, and the exchange of the two receptor tyrosine kinases is sufficient to convert the cellular response to Sema4D from pro- to anti-migratory and vice versa. This work identifies a novel mechanism by which plexin-mediated signaling can be regulated and explains how Sema4D can exert different biological activities through the differential association of its receptor with ErbB-2 and Met.     

Formation and temperature stability of G-quadruplex structures studied by electronic and vibrational circular dichroism spectroscopy combined with ab initio calculations

Variations in the structure of d(GGGA)(5) oligonucleotide in the presence of Li(+), Na(+), and K(+) ions and its temperature stability were studied using electronic and vibrational circular dichroism, IR absorption, and ab initio calculations with the Becke 3-Lee-Yang-Parr functional at the 6-31G** level. The samples were characterized by nondenaturing gel electrophoresis. Oligonucleotide d(GGGA)(5) in the presence of Li(+) forms a nonplanar single tetramer, with angles of 102 degrees and 171 degrees between neighboring guanine bases. This tetramer changes its geometry at temperatures >50 degrees C, but does not form a quadruplex structure. In the presence of Na(+), the d(GGGA)(5) structure was optimized to almost planar tetramers with an angle of 177 degrees between neighboring guanines. The spectral results suggest that it stacks into a quadruplex helical structure. This quadruplex structure decayed to a single tetramer at temperatures >60 degrees C. The Hartree-Fock energies imply that d(GGGA)(5) prefers to form complexes with Na(+) rather than Li(+). The d(GGGA)(5) structure in the presence of monovalent ions is stabilized against thermal denaturation in the order Li(+) < Na(+) < K(+).     

Pioglitazone, a PPAR-gamma ligand, exerts cytostatic/cytotoxic effects against cancer cells, that do not result from inhibition of proteasome

Thiazolidinediones are oral antidiabetic agents that activate peroxisome proliferator-activated receptor-gamma (PPAR-gamma) and exert potent antioxidant and anti-inflammatory properties. It has also been shown that PPAR-gamma agonists induce G0/G1 arrest and apoptosis of malignant cells. Some of these effects have been suggested to result from inhibition of proteasome activity in target cells. The aim of our studies was to critically evaluate the cytostatic/cytotoxic effects of one of thiazolidinediones (pioglitazone) and its influence on proteasome activity. Pioglitazone exerted dose-dependent cytostatic/cytotoxic effects in MIA PaCa-2 cells. Incubation of tumor cells with pioglitazone resulted in increased levels of p53 and p27 and decreased levels of cyclin D1. Accumulation of polyubiquitinated proteins within cells incubated with pioglitazone suggested dysfunction of proteasome activity. However, we did not observe any influence of pioglitazone on the activity of isolated proteasome and on the proteolytic activity in lysates of pioglitazone-treated MIA PaCa-2 cells. Further, treatment with pioglitazone did not cause an accumulation of fluorescent proteasome substrates in transfected HeLa cells expressing unstable GFP variants. Our results indicate that pioglitazone does not act as a direct or indirect proteasome inhibitor.