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71.
B Ruszczycki Z Szepesi G Wilczynski M Bijata K Kalita L Kaczmarek J Wlodarczyk 《BMC bioinformatics》2012,13(1):213
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. 相似文献
72.
Banach M Prymula K Jurkowski W Konieczny L Roterman I 《Journal of molecular modeling》2012,18(1):229-237
Mutations in proteins introduce structural changes and influence biological activity: the specific effects depend on the location
of the mutation. The simple method proposed in the present paper is based on a two-step model of in silico protein folding.
The structure of the first intermediate is assumed to be determined solely by backbone conformation. The structure of the
second one is assumed to be determined by the presence of a hydrophobic center. The comparable structural analysis of the
set of mutants is performed to identify the mutant-induced structural changes. The changes of the hydrophobic core organization
measured by the divergence entropy allows quantitative comparison estimating the relative structural changes upon mutation.
The set of antifreeze proteins, which appeared to represent the hydrophobic core structure accordant with “fuzzy oil drop”
model was selected for analysis. 相似文献
73.
Jablonska E Jablonski J Marcinczyk M Grabowska Z Piotrowski L 《Folia histochemica et cytobiologica / Polish Academy of Sciences, Polish Histochemical and Cytochemical Society》2008,46(2):177-183
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. 相似文献
74.
Understanding chlorophylls: central magnesium ion and phytyl as structural determinants 总被引:1,自引:0,他引:1
Fiedor L Kania A Myśliwa-Kurdziel B Orzeł Ł Stochel G 《Biochimica et biophysica acta》2008,1777(12):1491-1500
Phytol, a C20 alcohol esterifying the C-17(3) propionate, and Mg2+ ion chelated in the central cavity, are conservative structural constituents of chlorophylls. To evaluate their intramolecular structural effects we prepared a series of metal- and phytyl-free derivatives of bacteriochlorophyll a and applied them as model chlorophylls. A detailed spectroscopic study on the model pigments reveals meaningful differences in the spectral characteristics of the phytylated and non-phytylated pigments. Their analysis in terms of solvatochromism and axial coordination shows how the central Mg and phytyl residue shape the properties of the pigment. Surprisingly, the presence/absence of the central Mg has no effect on the solvatochromism of (bacterio)chlorophyll pi-electron system and the hydrophobicity of phytyl does not interfere with the first solvation shell of the chromophore. However, both residues significantly influence the conformation of the pigment macrocycle and the removal of either residue increases the macrocycle flexibility. The chelation of Mg has a flattening effect on the macrocycle whereas bulky phytyl residue seems to control the conformation of the chromophore via steric interactions with ring V and its substituents. The analysis of spectroscopic properties of bacteriochlorophyllide (free acid) shows that esterification of the C-17(3) propionate is necessary in chlorophylls because the carboxyl group may act as a strong chelator of the central Mg. These observations imply that the truncated chlorophylls used in theoretical studies are not adequate as models of native chromophores, especially when fine effects are to be modeled. 相似文献
75.
Xiong X Cui P Hossain S Xu R Warner B Guo X An X Debnath AK Cowburn D Kotula L 《Biochimica et biophysica acta》2008,1783(5):737-747
Here we report c-Abl kinase inhibition mediated by a phosphotyrosine located in trans in the c-Abl substrate, Abi1. The mechanism, which is pertinent to the nonmyristoylated c-Abl kinase, involves high affinity concurrent binding of the phosphotyrosine pY213 to the Abl SH2 domain and binding of a proximal PXXP motif to the Abl SH3 domain. Abi1 regulation of c-Abl in vivo appears to play a critical role, as demonstrated by inhibition of pY412 phosphorylation of the nonmyristoylated Abl by coexpression of Abi1. Pervanadate-induced c-Abl kinase activity was also reduced upon expression of the wild type Abi1 but not by expression of the Y213 to F213 mutant Abi1 in LNCaP cells, which are naturally deficient in the regulatory pY213. Our findings suggest a novel mechanism by which Abl kinase is regulated in cells. 相似文献
76.
UDP-glucose pyrophosphorylase (UGPase) is an important enzyme in the production (and conversions) of UDP-glucose, a key precursor for carbohydrate biosynthesis. cDNAs corresponding to two UGPase isozymes in Arabidopsis were overexpressed in Escherichia coli and, subsequently, the recombinant proteins were purified and characterized. Both proteins were highly conserved, sharing 93% identity. Based on crystal structure-derived images, the main amino acid differences mapped to N- and C-termini domains, but not to central active site region. The two proteins existed mainly as monomers, and they had similar molecular masses of ca. 53 kDa. However, comparison of molecular masses of UGPases from Arabidopsis root and leaf extracts revealed that the root protein was slightly larger, suggesting a post-translational modification. Specific activity of the purified UGPase-1 was ca. 10-30% lower than that of UGPase-2, depending on direction of the reaction, whereas its K(m) values with all substrates in both directions of the reaction were consistently ca. twice lower than those of UGPase-2 (0.03-0.14 mM vs. 0.07-0.36 mM, respectively). Both proteins were "true" UGPases, and had no activity with ADP-glucose/ATP or galactose-1-P. Equilibrium constant for both proteins was ca. 0.3, suggesting preference for the pyrophosphorolysis direction of the reaction. The data are discussed with respect to potential roles of UGPase in carbohydrate synthesis/metabolism in Arabidopsis. 相似文献
77.
78.
Diversity of rotifers from northeastern U.S.A. bogs with new species records for North America and New England 总被引:1,自引:1,他引:0
In order to assess the effects of pollution on recruitment of brown trout (Salmo trutta f. fario L.) exposure experiments with brown trout early life stages were performed in two differently contaminated small streams near Stuttgart, southwest Germany, and in a control situation in the laboratory. Pollution in the more polluted stream is mainly due to effluents of municipal sewage treatment plants and to the influx of surface waters from areas of intense agriculture activity. Additionally, the water carries high particle loads, especially after rainfall events. Water quality of the less polluted stream is occasionally influenced by agriculture activity in the vicinity. For the exposure of trout early life stages incubators were used, which allowed frequent examinations without serious disturbance of the exposed organisms and thus the development could be monitored over time. Compared to the less polluted stream and the control, in the more polluted stream high mortality rates, the lowest hatching success, and lowest values for growth occurred. In the less polluted stream, mortality rates were comparably low in prehatching stages, but high in hatchlings and juveniles due to heavy infestations with protozoic ectoparasites Chilodonella cyprini (Moroff, 1902) and Ichthyobodo necator (Henneguy, 1883). However, pollution-related effects were not detected in this stream. Differences in developmental rates between the different treatments were correlated with different water temperatures in the two streams and the control. For the more polluted stream, previous studies have indicated embryotoxic potentials mediated by pollutants. The present study indicates that in this steam, additionally, fine solids which infiltrate stream gravels may seriously affect development of brown trout early life stages. 相似文献
79.
Juszczyk Paulina Łankiewicz Leszek Kołodziejczyk Aleksandra S. 《International journal of peptide research and therapeutics》2002,9(4-5):187-192
Summary A convenient route to amino acid-based orthogonally protected 1,2-diamines starting from materials readily available for a
peptide chemist is presented. The key step of the procedure is the Mitsunobu reaction ofN-protected aminoalcohol, obtained by the reduction of commercially available Z- or Boc-protected amino acid, with imidodicarbonate
or sulfonylcarbamate related to standard amino-protecting groups used in peptide chemistry yielding triprotected vicinal diamines. 相似文献
80.
Cheng-yi Lii Chia-ding Liao Leszek Stobinski Piotr Tomasik 《Carbohydrate polymers》2002,49(4):449-456
Cassava, corn, high amylose corn, potato, rice Indica, rice Japonica, sweet potato, waxy corn, and wheat starches were exposed to low-pressure ammonia, hydrogen, and oxygen plasma. In every case, depolymerization of the starch polysaccharides was noted. The extent of the depolymerization depended on the nature of the starch as well as the type of plasma applied. Among three fractions of polysaccharides distinguished by their molecular weight average, the fraction of the highest molecular weight suffered the most efficient depolymerization. The relative depolymerization for the middle- and low-molecular fractions of polysaccharides was found to be starch and plasma specific. The chemical character of the plasma had very little influence on the starch polysaccharides. Only subtle oxidation effects were observed in oxygen plasma. Low-pressure glow plasma treatment appeared to be a convenient tool for a waste-less dextrinization of starch. Manipulation of the plasma variety and the time of exposure resulted in a wide spectrum of dextrins of various molecular weights and paste-forming properties. 相似文献