Comparison of different models of motion in a crowded environment: a Monte Carlo study.

In this paper we investigate the motion of molecules in crowded environments for two dramatically different types of molecular transport. The first type is realized by the dynamic lattice liquid model, which is based on a cooperative movement concept and thus, the motion of molecules is highly correlated. The second one corresponds to a so-called motion of a single agent where the motion of molecules is considered as a random walk without any correlation with other moving elements. The crowded environments are modeled as a two-dimensional triangular lattice with fixed impenetrable obstacles. Our simulation results indicate that the type of transport has an impact on the dynamics of the system, the percolation threshold, critical exponents, and on molecules' trajectories.

Identification of functional, short-lived isoform of linker for activation of T cells (LAT).

Linker for activation of T cells (LAT) is a transmembrane adaptor protein playing a key role in the development, activation and maintenance of peripheral homeostasis of T cells. In this study we identified a functional isoform of LAT. It originates from an intron 6 retention event generating an in-frame splice variant of LAT mRNA denoted as LATi6. Comparison of LATi6 expression in peripheral blood leukocytes of human and several other mammalian species revealed that it varied from being virtually absent in the mouse to being predominant in the cow. Analysis of LAT isoform frequency expressed from minigene splicing reporters carrying loss- or gain-of-function point mutations within intronic polyguanine sequences showed that these elements are critical for controlling the intron 6 removal. The protein product of LATi6 isoform (LATi6) ectopically expressed in LAT-deficient JCam 2.5 cell line localized correctly to subcellular compartments and supported T-cell receptor signaling but differed from the canonical LAT protein by displaying a shorter half-life and mediating an increased interleukin-2 secretion upon prolonged CD3/CD28 crosslinking. Altogether, our data suggest that the appearance of LATi6 isoform is an evolutionary innovation that may contribute to a more efficient proofreading control of effector T-cell response.

Prevalence and distribution of Dirofilaria repens Railliet et Henry, 1911 in dogs in Poland.

In 2011-2013 1588 samples of dogs' blood were examined for dirofilariosis using Knott method, as well as the Kingston and Morton method. The species of microfilariae was determined on the basis of morphometric characteristics. Samples were also examined using the Canine Heartworm Antigen Test. Positive samples were examined using a multiplex PCR assay for species confirmation. Microfilariae belonging to the species D. repens were found in the blood samples of dogs from all the provinces of Poland. The mean prevalence of this species observed in Poland was 11.7%. The range of intensity of infection was counted using the number of microfilariae found in 60 microl of blood amounted to between 1 and 158, and the mean intensity was 18 microfilariae. Microfilariae and antigens of D. immitis were not found in any examined blood samples.

A personalised approach to prostate cancer screening based on genotyping of risk founder alleles.

BACKGROUND: To evaluate whether genotyping for 18 prostate cancer founder variants is helpful in identifying high-risk individuals and for determining optimal screening regimens. METHODS: A serum PSA level was measured and a digital rectal examination (DRE) was performed on 2907 unaffected men aged 40-90. Three hundred and twenty-three men with an elevated PSA (≥4 ng ml⁻¹) or an abnormal DRE underwent a prostate biopsy. All men were genotyped for three founder alleles in BRCA1 (5382insC, 4153delA and C61G), for four alleles in CHEK2 (1100delC, IVS2+1G>A, del5395 and I157T), for one allele in NBS1 (657del5), for one allele in HOXB13 (G84E), and for nine low-risk single-nucleotide polymorphisms (SNPs). RESULTS: On the basis of an elevated PSA or an abnormal DRE, prostate cancer was diagnosed in 135 of 2907 men (4.6%). In men with a CHEK2 missense mutation I157T, the cancer detection rate among men with an elevated PSA or an abnormal DRE was much higher (10.2%, P=0.0008). The cancer detection rate rose with the number of SNP risk genotypes observed from 1.2% for men with no variant to 8.6% for men who carried six or more variants (P=0.04). No single variant was helpful on its own in predicting the presence of prostate cancer, however, the combination of all rare mutations and SNPs improved predictive power (area under the curve=0.59; P=0.03). CONCLUSION: These results suggest that testing for germline CHEK2 mutations improves the ability to predict the presence of prostate cancer in screened men, however, the clinical utility of incorporating DNA variants in the screening process is marginal.

An inherited NBN mutation is associated with poor prognosis prostate cancer.

BACKGROUND: To establish the contribution of eight founder alleles in three DNA damage repair genes (BRCA1, CHEK2 and NBS1) to prostate cancer in Poland, and to measure the impact of these variants on survival among patients. METHODS: Three thousand seven hundred fifty men with prostate cancer and 3956 cancer-free controls were genotyped for three founder alleles in BRCA1 (5382insC, 4153delA, C61G), four alleles in CHEK2 (1100delC, IVS2+1G>A, del5395, I157T), and one allele in NBS1 (657del5). RESULTS: The NBS1 mutation was detected in 53 of 3750 unselected cases compared with 23 of 3956 (0.6%) controls (odds ratio (OR)=2.5; P=0.0003). A CHEK2 mutation was seen in 383 (10.2%) unselected cases and in 228 (5.8%) controls (OR=1.9; P<0.0001). Mutation of BRCA1 (three mutations combined) was not associated with the risk of prostate cancer (OR=0.9; P=0.8). In a subgroup analysis, the 4153delA mutation was associated with early-onset (age ≤ 60 years) prostate cancer (OR=20.3, P=0.004). The mean follow-up was 54 months. Mortality was significantly worse for carriers of a NBS1 mutation than for non-carriers (HR=1.85; P=0.008). The 5-year survival for men with an NBS1 mutation was 49%, compared with 72% for mutation-negative cases. CONCLUSION: A mutation in NBS1 predisposes to aggressive prostate cancer. These data are relevant to the prospect of adapting personalised medicine to prostate cancer prevention and treatment.

Spectrin-based skeleton as an actor in cell signaling.

This review focuses on the recent advances in functions of spectrins in non-erythroid cells. We discuss new data concerning the commonly known role of the spectrin-based skeleton in control of membrane organization, stability and shape, and tethering protein mosaics to the cellular motors and to all major filament systems. Particular effort has been undertaken to highlight recent advances linking spectrin to cell signaling phenomena and its participation in signal transduction pathways in many cell types.

Expression of decorin in esophageal cancer in relation to the expression of three isoforms of transforming growth factor-beta (TGF-beta1, -beta2, and -beta3) and matrix metalloproteinase-2 activity.

To determine the role of the reactive stroma in cancer progression, we investigated decorin (DCN) and transforming growth factor-beta (TGF-beta expression, and matrix metalloproteinase-2 (MMP-2) activity in the tumorous esophagus. We found statistically insignificantly decreased levels of DCN expression in the pathological tissues. No obvious alterations in TGF-beta expression were noticed. The highly significant increase in MMP-2 activity in cancers did not result in elevated levels of TGF-beta dimers. Therefore, the system of TGF-beta liberation from its complex with DCN by activated MMP-2 does not seem to contribute to esophageal cancerogenesis, although this hypothesis should be reevaluated with a larger study group.

Synapsin I-mediated interaction of brain spectrin with synaptic vesicles.

We have established a new binding assay in which 125I-labeled synaptic vesicles are incubated with brain spectrin covalently immobilized on cellulosic membranes in a microfiltration apparatus. We obtained saturable, high affinity, salt- (optimum at 50-70 mM NaCl) and pH- (optimum at pH 7.5-7.8) dependent binding. Nonlinear regression analysis of the binding isotherm indicated one site binding with a Kd = 59 micrograms/ml and a maximal binding capacity = 1.9 micrograms vesicle protein per microgram spectrin. The fact that the binding of spectrin was via synapsin was demonstrated in three ways. (a) Binding of synaptic vesicles to immobilized spectrin was eliminated by prior extraction with 1 M KCl. When the peripheral membrane proteins in the 1 M KCl extract were separated by SDS-PAGE, transferred to nitrocellulose paper and incubated with 125I-brain spectrin, 96% of the total radioactivity was associated with five polypeptides of 80, 75, 69, 64, and 40 kD. All five polypeptides reacted with an anti-synapsin I polyclonal antibody, and the 80- and 75-kD polypeptides comigrated with authentic synapsin Ia and synapsin Ib. The 69- and 64-kD polypeptides are either proteolytic fragments of synapsin I or represent synapsin IIa and synapsin IIb. (b) Pure synapsin I was capable of competitively inhibiting the binding of radioiodinated synaptic vesicles to immobilized brain spectrin with a Kl = 46 nM. (c) Fab fragments of anti-synapsin I were capable of inhibiting the binding of radioiodinated synaptic vesicles to immobilized brain spectrin. These three observations clearly establish that synapsin I is a primary receptor for brain spectrin on the cytoplasmic surface of the synaptic vesicle membrane.

A large germline deletion in the Chek2 kinase gene is associated with an increased risk of prostate cancer.

BACKGROUND: Germline mutations in the Chek2 kinase gene (CHEK2) have been associated with a range of cancer types. Recently, a large deletion of exons 9 and 10 of CHEK2 was identified in several unrelated patients with breast cancer of Czech or Slovak origin. The geographical and ethnic extent of this founder allele has not yet been determined. PARTICIPANTS AND METHODS: We assayed for the presence of this deletion, and of three other CHEK2 founder mutations, in 1864 patients with prostate cancer and 5496 controls from Poland. RESULTS: The deletion was detected in 24 of 5496 (0.4%) controls from the general population, and is the most common CHEK2 truncating founder allele in Polish patients. The deletion was identified in 15 of 1864 (0.8%) men with unselected prostate cancer (OR 1.9; 95% CI 0.97 to 3.5; p = 0.09) and in 4 of 249 men with familial prostate cancer (OR 3.7; 95% CI 1.3 to 10.8; p = 0.03). These ORs were similar to those associated with the other truncating mutations (IVS2+1G-->A, 1100delC). CONCLUSION: A large deletion of exons 9 and 10 of CHEK2 confers an increased risk of prostate cancer in Polish men. The del5395 founder deletion might be present in other Slavic populations, including Ukraine, Belarus, Russia, Baltic and Balkan countries. It will be of interest to see to what extent this deletion is responsible for the burden of prostate cancer in other populations.

Common regions of deletion in chromosome regions 3p12 and 3p14.2 in primary clear cell renal carcinomas.

Nearly all clear cell renal cell carcinomas (RCCs) exhibit loss of alleles on the short arm of chromosome 3. Loss and mutation at the von Hippel-Lindau (VHL) gene at 3p25 probably occurs in most RCCs and, since the VHL gene was recently cloned, data on VHL involvement in RCCs is accumulating. However, the region 3p14-p12, a region that contains the familial RCC-associated t(3;8)(p14.2;q24) chromosome translocation and the small cell lung carcinoma-associated homozygous deletion at 3p13-12, has also been reported to exhibit allele loss in a large fraction of RCCs. In order to focus future studies on potential suppressor genes in the 3p14-p12 region, we have studied allele loss in 30 RCCs with 9 polymorphic simple sequence repeat markers spanning 3p21.1-p12. Partial losses in the 3p21-p12 region were observed, allowing determination of common regions of loss of heterozygosity overlap in 15 RCCs. Results suggested that most RCCs exhibit loss in a region which brackets the t(3;8) familial chromosome translocation at 3p14.2, and some show additional deletions within the U2020 small cell lung carcinoma deletion at 3p12.

NBS1 is a prostate cancer susceptibility gene.

To evaluate whether an inactivating mutation in the gene for the Nijmegen breakage syndrome (NBS1) plays a role in the etiology of prostate cancer, we compared the prevalence of the 657del5 NBS1 founder allele in 56 patients with familial prostate cancer, 305 patients with nonfamilial prostate cancer, and 1500 control subjects from Poland. Loss of heterozygosity analysis also was performed on DNA samples isolated from 17 microdissected prostate cancers, including 8 from carriers of the 657del5 mutation. The NBS1 founder mutation was present in 5 of 56 (9%) patients with familial prostate cancer (odds ratio, 16; P < 0.0001), 7 of 305 (2.2%) patients with nonfamilial prostate cancer (odds ratio, 3.9; P = 0.01), and 9 of 1500 control subjects (0.6%). The wild-type NBS1 allele was lost in seven of eight prostate tumors from carriers of the 657del5 allele, but loss of heterozygosity was seen in only one of nine tumors from noncarriers (P = 0.003). These findings suggest that heterozygous carriers of the NBS1 founder mutation exhibit increased susceptibility to prostate cancer and that the cancers that develop in the prostates of carriers are functionally homozygous for the mutation.

Loss of heterozygosity at the familial RCC t(3;8) locus in most clear cell renal carcinomas.

Previously, we had observed that more than 80% of clear cell renal carcinomas (RCCs) exhibited loss of heterozygosity (LOH) between the microsatellite markers D3S1285 (in 3p14.1) and D3S1295 (in 3p21.1), a region which includes the protein tyrosine phosphatase gamma locus (PTPRG locus, PTP gamma gene) and the 3p14.2 break of the familial RCC-associated translocation, t(3;8)(p14.2;q24), which has been hypothesized to affect expression of an RCC suppressor gene or oncogene. Using seven microsatellite markers and four markers derived from a PTPRG YAC contig, we have further delineated the 3p14.2 region of LOH in RCCs. Eighty-nine % of clear cell RCCs (31 of 35) showed a common region of loss between the D3S1481 and D3S1312 loci which flank the 3p14.2 t(3;8) translocation breakpoint and the PTP gamma gene. The PTP gamma gene occupies approximately 780 kilobase pairs between markers D3S1480 and D3S1312, with its currently defined 5' end greater than 200 kilobase pairs centromeric to the 3p14.2 translocation break. Although most of the RCCs with LOH between D3S1481 and D3S1312 loci have lost at least a portion of one PTP gamma allele, we have tested all known exons of the remaining PTP gamma gene in a number of the kidney tumors and have not observed mutations. Thus, there may be another gene in the vicinity of the 3p14.2 break that is important not only in the familial RCCs in the t(3;8) family but in the majority of clear cell RCCs.

Labelling of erythrocyte spectrin in situ with phenylisothiocyanate.

The labelling of erythrocyte spectrin in situ with the hydrophobic reagent phenylisothiocyanate (Sigrist, H. and Zahler, P. (1978) FEBS Lett. 95, 116-120) is studied. Spectrin isolated from erythrocytes which have been incubated with phenylisothiocyanate is covalently modified by the probe. The modification in the spectrin molecule is stable under an excess of nucleophile in alkaline conditions. The labelling is very little or not affected by preincubation of erythrocytes of membranes with the polar, structural analogue of phenylisothiocyanate, p-sulfophenylisothiocyanate. When erythrocyte ghosts are subjected to labelling, a substantial increase in the degree of spectrin modification is observed. Subunits of labelled spectrin separated electrophoretically show similar amounts of attached label.

The effect of nonadec(en)ylresorcinol on the fluidity of liposome and erythrocyte membranes.

The effect of alk(en)ylresorcinol homologs (5-(n-nonadecyl)- and 5-(n-nonadecenyl)resorcinol) on the mobility of 5-doxyl- and 12-doxylstearate spin probes incorporated into DMPC, DMPC-cholesterol and erythrocyte membranes was studied. It was found that both homologs affect the properties of hydrophobic environment of the membranes: (1) In DMPC vesicles both homologs induce an increase in the order parameter of 5-doxylstearate at temperatures of Tc and above. (2) At higher concentrations of both homologs a decrease in mobility of the 12-doxylstearate was also observed. (3) In the presence of cholesterol in the liposome membrane the influence of alk(en)ylresorcinols on the mobility of spin probes was much greater, depending on the cholesterol content and the position of the probe in the bilayer. (4) In natural membranes (erythrocyte ghosts) both alkyl- and alkenylresorcinols induced a decrease of mobility in the region of 12-doxylstearate as well as in the region closer to the polar head groups of lipids (5-doxylstearate).

Interaction of spectrin with phospholipids. Quenching of spectrin intrinsic fluorescence by phospholipid suspensions.

Phospholipid suspensions prepared of phosphatidylethanolamine, phosphatidylserine and their mixtures are able to influence the intrinsic protein fluorescence of spectrin. In the case of phosphatidylethanolamine suspension up to 75% of protein fluorescence can be quenched. The interaction of phospholipid aggregates with spectrin is modulated by pH and ionic strength. Phospholipids, particularly phosphatidylethanolamine display a 'stabilizing' effect against the changes of protein fluorescence induced by increasing ionic strength and by thermal denaturation.

Ankyrin inhibits binding of erythrocyte spectrin to phospholipid vesicles.

The studies on binding of erythrocyte spectrin to frozen and thawed phospholipid liposomes and its inhibition by ankyrin were performed. It was found that ankyrin inhibited up to 60% binding of spectrin by phosphatidylethanolamine/phosphatidylcholine vesicles. It was able to dissociate up to 40% of spectrin from this complex. Ankyrin inhibition of binding of phosphatidylserine/phosphatidylcholine vesicles by spectrin, although much lower, was also observed.

Dynamic Monte Carlo simulations of globular protein folding. Model studies of in vivo assembly of four helix bundles and four member beta-barrels.

As part of an ongoing series of dynamic Monte Carlo simulations of globular protein folding, the nature of the folding pathway, of model four-member beta-barrels and four-helix bundles, under highly idealized conditions in vivo, has been examined. The ribosome is crudely modeled as an inert hard wall on to which the model protein chain is attached. Three cases are considered in detail. The first corresponds to post-translational assembly in which the fully synthesized chain is tethered to the wall and starts out under strongly denaturing conditions. The system is cooled down, and the chain is allowed to fold. Interestingly, the helical motif prefers to assemble parallel to the wall, whereas the beta-barrel, predominantly assembles with its principal axis perpendicular to the wall. In the former case, the dominant intermediate, the helical hairpin, is different from that in free solution, a three-helix bundle. The wall acts to reduce the expanse of configuration space that must be searched and aids in folding. Two situations that might lead to co-translational folding are also simulated. In the first case, to eliminate wall effects, the chain is slowly synthesized in free solution, and in the second case, it is slowly synthesized from the wall. In all cases, the chains are observed to fold post-translationally. While partially folded intermediates are observed during synthesis, they lack the stability to survive until chain synthesis is complete. The implications of these results for the folding in vivo of real protein chains is discussed, and a model of multiple domain protein folding is proposed.

Dynamic Monte Carlo simulations of globular protein folding/unfolding pathways. II. Alpha-helical motifs.

Dynamic Monte Carlo simulations of the folding pathways of alpha-helical protein motifs have been undertaken in the context of a diamond lattice model of globular proteins. The first question addressed in the nature of the assembly process of an alpha-helical hairpin. While the hairpin could, in principle, be formed via the diffusion-collision-adhesion of isolated performed helices, this is not the dominant mechanism of assembly found in the simulations. Rather, the helices that form native hairpins are constructed on-site, with folding initiating at or near the turn in almost all cases. Next, the folding/unfolding pathways of four-helix bundles having tight bends and one and two long loops in the native state are explored. Once again, an on-site construction mechanism of folding obtains, with a hairpin forming first, followed by the formation of a three-helix bundle, and finally the fourth helix of the native bundle assembles. Unfolding is essentially the reverse of folding. A simplified analytic theory is developed that reproduces the equilibrium folding transitions obtained from the simulations remarkably well and, for the dominant folding pathway, correctly identifies the intermediates seen in the simulations. The analytic theory provides the free energy along the reaction co-ordinate and identifies the transition state for all three motifs as being quite close to the native state, with three of the four helices assembled, and approximately one turn of the fourth helix in place. The transition state is separated from the native conformation by a free-energy barrier of mainly energetic origin and from the denatured state by a barrier of mainly entropic origin. The general features of the folding pathway seen in all variants of the model four-helix bundles are similar to those observed in the folding of beta-barrel, Greek key proteins; this suggests that many of the qualitative aspects of folding are invariant to the particular native state topology and secondary structure.

ESR and monolayer study of the localization of coenzyme Q10 in artificial membranes.

The data obtained from the ESR experiments show a complex, depth dependent effect of CoQ10 on the lipid molecules mobility in the bilayer. These effects depend both on its concentration and the temperature. CoQ10 disturbs not only the hydrophobic core of the membrane but also the region close to the hydrophilic headgroups of phospholipids. Both these effects could be explained by the fact that the high hydrophobicity of CoQ10 causes the molecules to position itself in the interior of the bilayer, but at the same time its water seeking headgroup is located close to the region of the polar headgrops of membrane lipids. The presence of CoQ10 in the hydrophobic core has further implications on the properties of membrane intrinsic domain. Results of monolayer experiments indicate that CoQ10 may form aggregates when mixed with PC molecules in the lipid hydrocarbon chain-length dependent manner. CoQ10 is not fully miscible with DMPC or DPPC but it is well miscible with the long-chain DSPC molecules. Our suggestion is that CoQ10 when present in long-chain phospholipid bilayer, interacts with saturated fatty acyl-chains and adapt the structure which allows such interactions: either parallel to the saturated acyl chains or "pseudo-ring" conformation resembling sterol structure.

Structure, physicochemical and biological properties of new complex salt of aqua-(nitrilotriacetato-N,O,O',O")-oxidovanadium(IV) anion with 1,10-phenanthrolinium cation.

The crystal structure of new 1,10-phenathrolin-1-ium aqua-(nitrilotriacetato-N,O,O',O")-oxidovanadium(IV) semihydrate of molecular formula (phenH)[VO(NTA)(H2O)]∙1/2H2O was determined. This is the first example of structurally characterized compound that comprises a distinctly separated, monomeric [VO(NTA)(H2O)](-) coordination entity. The crystallographic measurements have subsequently been complemented by the IR spectroscopic characterization and thermal analysis. Furthermore, the electrochemical (cyclic voltammetry) as well as spectrophotometric (UV-vis) studies revealed that the compound is capable of scavenging the superoxide free radicals (O2(-)) as well as stable organic radicals i.e. 2,2'-azinobis(3-ethylbenzothiazoline-6 sulfonic acid) cation radical (ABTS(+)) and 2,2-diphenyl-1-picrylhydrazyl radical (DPPH), but its reactivity towards radicals is lower than that of VOSO4. Finally, biological properties of the complex in the range of 1-100 µM were investigated in relation to its cytoprotective activity against the oxidative damage generated exogenously by using hydrogen peroxide in the hippocampal neuronal HT22 cell line (the MTT and LDH tests). It has been established that in contrast to VOSO4 the title compound protects the HT22 from the oxidative damage. The paper presents a new perspective for oxidovanadium(IV) complexes as candidates for novel, low-molecular mass cytoprotective agents.