Suppression subtractive hybridization profiles of radial growth phase and metastatic melanoma cell lines reveal novel potential targets

Background: Melanoma progression occurs through three major stages: radial growth phase (RGP), confined to the epidermis; vertical growth phase (VGP), when the tumor has invaded into the dermis; and metastasis. In this work, we used suppression subtractive hybridization (SSH) to investigate the molecular signature of melanoma progression, by comparing a group of metastatic cell lines with an RGP-like cell line showing characteristics of early neoplastic lesions including expression of the metastasis suppressor KISS1, lack of alpha v beta 3-integrin and low levels of RHOC. Methods: Two subtracted cDNA collections were obtained, one (RGP library) by subtracting the RGP cell line (WM1552C) cDNA from a cDNA pool from four metastatic cell lines (WM9, WM852, 1205Lu and WM1617), and the other (Met library) by the reverse subtraction. Clones were sequenced and annotated, and expression validation was done by Northern blot and RT-PCR. Gene Ontology annotation and searches in large-scale melanoma expression studies were done for the genes identified. Results: We identified 367 clones from the RGP library and 386 from the Met library, of which 351 and 368, respectively, match human mRNA sequences, representing 288 and 217 annotated genes. We confirmed the differential expression of all genes selected for validation. In the Met library, we found an enrichment of genes in the growth factors/receptor, adhesion and motility categories whereas in the RGP library, enriched categories were nucleotide biosynthesis, DNA packing/repair, and macromolecular/vesicular trafficking. Interestingly, 19% of the genes from the RGP library map to chromosome 1 against 4% of the ones from Met library. Conclusion: This study identifies two populations of genes differentially expressed between melanoma cell lines from two tumor stages and suggests that these sets of genes represent profiles of less aggressive versus metastatic melanomas. A search for expression profiles of melanoma in available expression study databases allowed us to point to a great potential of involvement in tumor progression for several of the genes identified here. A few sequences obtained here may also contribute to extend annotated mRNAs or to the identification of novel transcripts.

Er : YAG laser, ultrasonic system, and curette produce different profiles on dentine root surfaces: An in vitro study

Objective: The aim of the present study was to compare the in vitro effects of the Er:YAG laser, an ultrasonic system, and manual curette on dentine root surface by roughness and micro-morphological analysis. Materials and Methods: Thirty-six flattened bovine roots were randomly assigned to one of the following groups: group 1 (n = 12): Er: YAG laser ( 2940 nm), 120 mJ/pulse, 10 Hz, 8.4 J/cm(2); group 2 ( n = 12): ultrasonic system; and group 3 ( n = 12): manual curette. The mean surface roughness (Ra) of each sample was measured using a profilometer before and after the treatments. The micro-morphology of the treated and untreated ( control) root surfaces was evaluated with scanning electron microscopy (SEM) at 50 x and 1000 x magnification. Results: Analysis with the profilometer showed that for equal times of instrumentation, the smoothest surfaces were produced by the Er: YAG laser and the ultrasonic system, followed by the curette ( p < 0.05). Morphological analyses demonstrated that treatment with the Er: YAG laser produced some areas with an irregular surface, craters, and ablation of the intertubular dentin. The smear layer was removed and dentine tubules were opened by both curettes and the ultrasonic system. The micro-morphology of the dentine root surface after ultrasonic treatment, however, demonstrated randomly distributed areas cratering. Conclusion: All instruments increased the roughness of the dentine root surface after treatment; however, the curette produced rougher surfaces than the other devices. SEM analysis revealed distinct root surface profiles produced by the three devices.

Synergistic effect of simvastatin and ezetimibe on lipid and pro-inflammatory profiles in pre-diabetic subjects

Background: Ezetimibe specifically blocks the absorption of dietary and biliary cholesterol and plant sterols. Synergism of ezetimibe-statin therapy on LDL-cholesterol has been demonstrated, but data concerning the pleiotropic effects of this combination are controversial. Objective: This open-label trial evaluated whether the combination of simvastatin and ezetimibe also results in a synergistic effect that reduces the pro-inflammatory status of pre-diabetic subjects. Methods: Fifty pre-diabetic subjects were randomly assigned to one of 2 groups, one receiving ezetimibe (10 mg/day), the other, simvastatin (20 mg/d) for 12 weeks, followed by an additional 12-week period of combined therapy. Blood samples were collected at baseline, 12 and 24 weeks. RESULTS: Total cholesterol, LDL-cholesterol and apolipoprotein B levels decreased in all the periods analyzed (p < 0.01), but triglycerides declined significantly only after combined therapy. Both drugs induced reductions in C-reactive protein, reaching statistical significance after combining ezetimibe with the simvastatin therapy (baseline 0.59 +/- 0.14, simvastatin monotherapy 0.48 +/- 0.12 mg/dL and 0.35 +/- 0.12 mg/dL, p < 0.023). Such a reduction was independent of LDL-cholesterol change. However, mean levels of TNF-alpha and interleukin-6 and leukocyte count did not vary during the whole study. Conclusion: Expected synergistic lowering effects of a simvastatin and ezetimibe combination on LDL-cholesterol, apolipoprotein B and triglycerides levels were confirmed in subjects with early disturbances of glucose metabolism. We suggest an additive effect of this combination also on inflammatory status based on the reduction of C-reactive protein. Attenuation of pro-inflammatory conditions may be relevant in reducing cardiometabolic risk.

Sequential analysis of global gene expression profiles in immature and in vitro matured bovine oocytes: potential molecular markers of oocyte maturation

Background: Without intensive selection, the majority of bovine oocytes submitted to in vitro embryo production (IVP) fail to develop to the blastocyst stage. This is attributed partly to their maturation status and competences. Using the Affymetrix GeneChip Bovine Genome Array, global mRNA expression analysis of immature (GV) and in vitro matured (IVM) bovine oocytes was carried out to characterize the transcriptome of bovine oocytes and then use a variety of approaches to determine whether the observed transcriptional changes during IVM was real or an artifact of the techniques used during analysis. Results: 8489 transcripts were detected across the two oocyte groups, of which similar to 25.0% (2117 transcripts) were differentially expressed (p < 0.001); corresponding to 589 over-expressed and 1528 under-expressed transcripts in the IVM oocytes compared to their immature counterparts. Over expression of transcripts by IVM oocytes is particularly interesting, therefore, a variety of approaches were employed to determine whether the observed transcriptional changes during IVM were real or an artifact of the techniques used during analysis, including the analysis of transcript abundance in oocytes in vitro matured in the presence of a-amanitin. Subsets of the differentially expressed genes were also validated by quantitative real-time PCR (qPCR) and the gene expression data was classified according to gene ontology and pathway enrichment. Numerous cell cycle linked (CDC2, CDK5, CDK8, HSPA2, MAPK14, TXNL4B), molecular transport (STX5, STX17, SEC22A, SEC22B), and differentiation (NACA) related genes were found to be among the several over-expressed transcripts in GV oocytes compared to the matured counterparts, while ANXA1, PLAU, STC1and LUM were among the over-expressed genes after oocyte maturation. Conclusion: Using sequential experiments, we have shown and confirmed transcriptional changes during oocyte maturation. This dataset provides a unique reference resource for studies concerned with the molecular mechanisms controlling oocyte meiotic maturation in cattle, addresses the existing conflicting issue of transcription during meiotic maturation and contributes to the global goal of improving assisted reproductive technology.

Cyclic variability of the circumstellar disk of the Be star zeta Tauri I. Long-term monitoring observations

Context. Emission lines formed in decretion disks of Be stars often undergo long-term cyclic variations, especially in the violet-to-red (V/R) ratio of their primary components. The underlying structural and dynamical variations of the disks are only partly understood. From observations of the bright Be-shell star. Tau, the possibly broadest and longest data set illustrating the prototype of this behaviour was compiled from our own and archival observations. It comprises optical and infrared spectra, broad-band polarimetry, and interferometric observations. Aims. The dense, long-time monitoring permits a better separation of repetitive and ephemeral variations. The broad wavelength coverage includes lines formed under different physical conditions, i.e. different locations in the disk, so that the dynamics can be probed throughout much of the disk. Polarimetry and interferometry constrain the spatial structure. All together, the objective is a better understand the dynamics and life cycle of decretion disks. Methods. Standard methods of data acquisition, reduction, and analysis were applied. Results. From 3 V/R cycles between 1997 and 2008, a mean cycle length in Ha of 1400-1430 days was derived. After each minimum in V/R, the shell absorption weakens and splits into two components, leading to 3 emission peaks. This phase may make the strongest contribution to the variability in cycle length. There is no obvious connection between the V/R cycle and the 133-day orbital period of the not otherwise detected companion. V/R curves of different lines are shifted in phase. Lines formed on average closer to the central star are ahead of the others. The shell absorption lines fall into 2 categories differing in line width, ionization/excitation potential, and variability of the equivalent width. They seem to form in separate regions of the disk, probably crossing the line of sight at different times. The interferometry has resolved the continuum and the line emission in Br gamma and HeI 2.06. The phasing of the Br gamma emission shows that the photocenter of the line-emitting region lies within the plane of the disk but is offset from the continuum source. The plane of the disk is constant throughout the observed V/R cycles. The observations lay the foundation for the fully self-consistent, one-armed, disk-oscillation model developed in Paper II.

Development of a DNA-dosimeter system for monitoring the effects of solar-ultraviolet radiation

Solar radiation sustains and affects all life forms on Earth. In recent years, the increase in environmental levels of solar-UV radiation due to depletion of the stratospheric ozone layer, as a result of anthropogenic emission of destructive chemicals, has highlighted serious issues of social concern. This becomes still more dramatic in tropical and subtropical regions, where the intensity of solar radiation is higher. To better understand the impact of the harmful effects of solar-UV radiation on the DNA molecule, we developed a reliable biological monitoring system based on the exposure of plasmid DNA to artificial UV lamps and sunlight. The determination and quanti. cation of different types of UV photoproducts were performed through the use of specific DNA repair enzymes and antibodies. As expected, a significant number of CPDs and 6-4PPs was observed when the DNA-dosimeter system was exposed to increasing doses of UVB radiation. Moreover, CPDs could also be clearly detected in plasmid DNA when this system was exposed to either UVA or directly to sunlight. Interestingly, although less abundant, 6-4PPs and oxidative DNA damage were also generated after exposure to both UVA and sunlight. These results confirm the genotoxic potential of sunlight, reveal that UVA may also produce CPDs and 6-4PPs directly in naked DNA and demonstrate the applicability of a DNA-dosimeter system for monitoring the biological effects of solar-UV radiation.

FLUCTUATIONS AND INITIAL STATE GRANULARITY IN HEAVY ION COLLISIONS AND THEIR EFFECTS ON OBSERVABLES FROM HYDRODYNAMICS

A comparison is made between results obtained using smooth initial conditions and event-by-event initial conditions in the hydrodynamical description of relativistic nuclear collisions. Some new results on directed flow are also included.

Topology Studies of Hydrodynamics Using Two-Particle Correlation Analysis

The effects of fluctuating initial conditions are studied in the context of relativistic heavy ion collisions where a rapidly evolving system is formed. Two-particle correlation analysis is applied to events generated with the NEXSPHERIO hydrodynamic code, starting with fluctuating nonsmooth initial conditions (IC). The results show that the nonsmoothness in the IC survives the hydroevolution and can be seen as topological features of the angular correlation function of the particles emerging from the evolving system. A long range correlation is observed in the longitudinal direction and in the azimuthal direction a double peak structure is observed in the opposite direction to the trigger particle. This analysis provides clear evidence that these are signatures of the combined effect of tubular structures present in the IC and the proceeding collective dynamics of the hot and dense medium.

KINETICS VERSUS HYDRODYNAMICS: GENERALIZATION OF LANDAU/COOPER-FRYE PRESCRIPTION FOR FREEZE-OUT

The problem of spectra formation in hydrodynamic approach to A + A collisions is considered within the Boltzmann equations. It is shown analytically and illustrated by numerical calculations that the particle momentum spectra can be presented in the Cooper-R-ye form despite freeze-out is not sharp and has the finite temporal width. The latter is equal to the inverse of the particle collision rate at points (t(sigma) (r, p), r) of the maximal emission at a fixed momentum p. The set of these points forms the hypersurfaces t(sigma)(r,p) which strongly depend on the values of p and typically do not enclose completely the initially dense matter. This is an important difference from the standard Cooper-Frye prescription (CFp), with a common freeze-out hypersurface for all p, that affects significantly the predicted spectra. Also, the well known problem of CFp as for negative contributions to the spectra from non-space-like parts of the freeze-out hypersurface is naturally eliminated in this improved prescription.

Directed flow at midrapidity in event-by-event hydrodynamics

Fluctuations in the initial geometry of a nucleus-nucleus collision have been recently shown to result in a new type of directed flow (v(1)) that, unlike the usual directed flow, is also present at midrapidity. We compute this new v(1) versus transverse momentum and centrality for Au-Au collisions at RHIC using the hydrodynamic code NeXSPheRIO. We find that the event plane of v(1) is correlated with the angle of the initial dipole of the distribution, as predicted, though with a large dispersion. It is uncorrelated with the reaction plane. Our results are in excellent agreement with results inferred from STAR correlation data.

Intermediate motions and dipolar couplings as studied by Lee-Goldburg cross-polarization NMR: Hartmann-Hahn matching profiles

In this article, we evaluate the use of simple Lee-Goldburg cross-polarization (LG-CP) NMR experiments for obtaining quantitative information of molecular motion in the intermediate regime. In particular, we introduce the measurement of Hartmann-Hahn matching profiles for the assessment of heteronuclear dipolar couplings as well as dynamics as a reliable and robust alternative to the more common analysis of build-up curves. We have carried out dynamic spin dynamics simulations in order to test the method's sensitivity to intermediate motion and address its limitations concerning possible experimental imperfections. We further demonstrate the successful use of simple theoretical concepts, most prominently Anderson-Weiss (AW) theory, to analyze the data. We further propose an alternative way to estimate activation energies of molecular motions, based upon the acquisition of only two LG-CP spectra per temperature at different temperatures. As experimental tests, molecular jumps in imidazole methyl sulfonate, trimethylsulfoxonium iodide, and bisphenol A polycarbonate were investigated with the new method.

Identification of protein-coding and non-coding RNA expression profiles in CD34(+) and in stromal cells in refractory anemia with ringed sideroblasts

Background: Myelodysplastic syndromes (MDS) are a group of clonal hematological disorders characterized by ineffective hematopoiesis with morphological evidence of marrow cell dysplasia resulting in peripheral blood cytopenia. Microarray technology has permitted a refined high-throughput mapping of the transcriptional activity in the human genome. Non-coding RNAs (ncRNAs) transcribed from intronic regions of genes are involved in a number of processes related to post-transcriptional control of gene expression, and in the regulation of exon-skipping and intron retention. Characterization of ncRNAs in progenitor cells and stromal cells of MDS patients could be strategic for understanding gene expression regulation in this disease. Methods: In this study, gene expression profiles of CD34(+) cells of 4 patients with MDS of refractory anemia with ringed sideroblasts (RARS) subgroup and stromal cells of 3 patients with MDS-RARS were compared with healthy individuals using 44 k combined intron-exon oligoarrays, which included probes for exons of protein-coding genes, and for non-coding RNAs transcribed from intronic regions in either the sense or antisense strands. Real-time RT-PCR was performed to confirm the expression levels of selected transcripts. Results: In CD34(+) cells of MDS-RARS patients, 216 genes were significantly differentially expressed (q-value <= 0.01) in comparison to healthy individuals, of which 65 (30%) were non-coding transcripts. In stromal cells of MDS-RARS, 12 genes were significantly differentially expressed (q-value <= 0.05) in comparison to healthy individuals, of which 3 (25%) were non-coding transcripts. Conclusions: These results demonstrated, for the first time, the differential ncRNA expression profile between MDS-RARS and healthy individuals, in CD34(+) cells and stromal cells, suggesting that ncRNAs may play an important role during the development of myelodysplastic syndromes.

Method for cadmium and lead longitudinal profiles determination in hair by solid sampling graphite furnace atomic absorption spectrometry

This paper describes methods for the direct determination of Cd and Pb in hair segments (c.a. 5 mm similar to 80 mu g) by solid sampling graphite furnace atomic absorption spectrometry, becoming possible longitudinal profiles in a single strand of hair. To distinguish endogenous and exogenous content. strands of hair were washed by using two different procedures: IAEA protocol (acetone + water + acetone) and the combination of IAEA protocol with HCl washing (acetone + water + acetone + 0.1 mol l(-1) HCl). The concentration of Cd and Pb increased from the root Until the tip of hair washed according to IAEA protocol. However, when the strand of hair was washed using the combination of IAEA protocol and 0.1 mol l(-1) HCl, Cd concentrations decreased in all segments, and Pb concentrations decreased drastically near to the root (5 to 12 mm) and was systematically higher ill the end. The proposed method showed to be useful to assess the temporal variation to Cd and Pb exposure and call be Used for toxicological and environmental investigations. The limits of detection were 2.8 ng g(-1) for Cd and 40 ng g(-1) for Pb. The characteristic masses based oil integrated absorbance were 2.4 pg for Cd and 22 pg for Pb.

Continuous monitoring of ascorbate transport through neuroblastoma cells with a ruthenium oxide hexacyanoferrate modified microelectrode

The uptake of ascorbate by neuroblastoma cells using a ruthenium oxide hexacyanoferrate (RuOHCF)-modified carbon fiber disc (CFD) microelectrode (r = 14.5 mu m) was investigated. By use of the proposed electrochemical sensor the amperometric determination of ascorbate was performed at 0.0 V in minimum essential medium (MEM, pH = 7.2) with a limit of detection of 25 mu mol L(-1). Under the optimum experimental conditions, no interference from MEM constituents and reduced glutathione (used to prevent the oxidation of ascorbate during the experiments) was noticed. The stability of the RuOHCF-modified electrode response was studied by measuring the sensitivity over an extended period of time (120 h), a decrease of around 10% being noticed at the end of the experiment. The rate of ascorbate uptake by control human neuroblastoma SH-SY5Y cells, and cells transfected with wild-type Cu,Zn-superoxide dismutase (SOD WT) or with a mutant typical of familial amyotrophic lateral sclerosis (SOD G93A), was in agreement with the level of oxidative stress in these cells. The usefulness of the RuOHCF-modified microelectrode for in vivo monitoring of ascorbate inside neuroblastoma cells was also demonstrated.

Instantaneous characterization of vegetable oils via TAG and FFA profiles by easy ambient sonic-spray ionization mass spectrometry

A fast and reliable method is presented for the analysis of vegetable oils. Easy ambient sonic-spray ionization mass spectrometry (EASI-MS) is shown to efficiently desorb and ionize the main oil constituents from an inert surface under ambient conditions and to provide comprehensive triacylglyceride (TAG) and free fatty acid (FFA) profiles detected mainly as either [ TAG + Na](+) or [FFA - H](-) ions. EASI(+/-)-MS analysis is simple, easily implemented, requires just a tiny droplet of the oil and is performed without any pre-separation or chemical manipulation. It also causes no fragmentation of TAG ions hence diacylglyceride (DAG) and monoacylglyceride (MAG) profiles and contents can also be measured. The EASI(+/-)-MS profiles of TAG and FFA permit authentication and quality control and can be used, for instance, to access levels of adulteration, acidity, oxidation or hydrolysis of vegetable oils in general.