Showing papers by "University of Crete published in 2004"

Organic aerosol and global climate modelling: a review

Abstract: The present paper reviews existing knowledge with regard to Organic Aerosol (OA) of importance for global climate modelling and defines critical gaps needed to reduce the involved uncertainties. All pieces required for the representation of OA in a global climate model are sketched out with special attention to Secondary Organic Aerosol (SOA): The emission estimates of primary carbonaceous particles and SOA precursor gases are summarized. The up-to-date understanding of the chemical formation and transformation of condensable organic material is outlined. Knowledge on the hygroscopicity of OA and measurements of optical properties of the organic aerosol constituents are summarized. The mechanisms of interactions of OA with clouds and dry and wet removal processes parameterisations in global models are outlined. This information is synthesized to provide a continuous analysis of the flow from the emitted material to the atmosphere up to the point of the climate impact of the produced organic aerosol. The sources of uncertainties at each step of this process are highlighted as areas that require further studies.

Nitric oxide in inflammatory bowel disease: a universal messenger in an unsolved puzzle

Abstract: In recent years, nitric oxide (NO), a gas previously considered to be a potentially toxic chemical, has been established as a diffusible universal messenger that mediates cell-cell communication throughout the body. Constitutive and inducible NO production regulate numerous essential functions of the gastrointestinal mucosa, such as maintenance of adequate perfusion, regulation of microvascular and epithelial permeability, and regulation of the immune response. Up-regulation of the production of NO via expression of inducible nitric oxide synthase (iNOS) represents part of a prompt intestinal antibacterial response; however, NO has also been associated with the initiation and maintenance of inflammation in human inflammatory bowel disease (IBD). Recent studies on animal models of experimental IBD have shown that constitutive and inducible NO production seems to be beneficial during acute colitis, but sustained up-regulation of NO is detrimental. This fact is also supported by studies on mice genetically deficient in various NOS isoforms. However, the mechanism by which NO proceeds from being an indispensable homeostatic regulator to a harmful destructor remains unknown. Furthermore, extrapolation of data from animal colitis models to human IBD is questionable. The purpose of this review is to update our knowledge about the role of this universal mediator and the enzymes that generate it in the pathogenesis of IBD.

Antiproliferative and apoptotic effects of selective phenolic acids on T47D human breast cancer cells: potential mechanisms of action.

Abstract: Introduction The oncoprotective role of food-derived polyphenol antioxidants has been described but the implicated mechanisms are not yet clear. In addition to polyphenols, phenolic acids, found at high concentrations in a number of plants, possess antioxidant action. The main phenolic acids found in foods are derivatives of 4-hydroxybenzoic acid and 4-hydroxycinnamic acid.

Improvements in the hbvar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies

Abstract: HbVar (http://globin.cse.psu.edu/globin/hbvar/) is a relational database developed by a multi-center academic effort to provide up-to-date and high quality information on the genomic sequence changes leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Extensive information is recorded for each variant and mutation, including sequence alterations, biochemical and hematological effects, associated pathology, ethnic occurrence and references. In addition to the regular updates to entries, we report two significant advances: (i) The frequencies for a large number of mutations causing β-thalassemia in at-risk populations have been extracted from the published literature and made available for the user to query upon. (ii) HbVar has been linked with the GALA (Genome Alignment and Annotation database, available at http://globin.cse.psu.edu/gala/) so that users can combine information on hemoglobin variants and thalassemia mutations with a wide spectrum of genomic data. It also expands the capacity to view and analyze the data, using tools within GALA and the University of California at Santa Cruz (UCSC) Genome Browser.

Wolbachia-induced cytoplasmic incompatibility as a means for insect pest population control

Abstract: Biological control is the purposeful introduction of parasites, predators, and pathogens to reduce or suppress pest populations. Wolbachia are inherited bacteria of arthropods that have recently attracted attention for their potential as new biocontrol agents. Wolbachia manipulate host reproduction by using several strategies, one of which is cytoplasmic incompatibility (CI) [Stouthamer, R., Breeuwer, J. A. J. & Hurst, G. D. D. (1999) Annu. Rev. Microbiol. 53, 71–102]. We established Wolbachia-infected lines of the medfly Ceratitis capitata using the infected cherry fruit fly Rhagoletis cerasi as donor. Wolbachia induced complete CI in the novel host. Laboratory cage populations were completely suppressed by single releases of infected males, suggesting that Wolbachia-induced CI could be used as a novel environmentally friendly tool for the control of medfly populations. The results also encourage the introduction of Wolbachia into pest and vector species of economic and hygenic relevance to suppress or modify natural populations.

Mutations in a Human ROBO Gene Disrupt Hindbrain Axon Pathway Crossing and Morphogenesis

Abstract: The mechanisms controlling axon guidance are of fundamental importance in understanding brain development. Growing corticospinal and somatosensory axons cross the midline in the medulla to reach their targets and thus form the basis of contralateral motor control and sensory input. The motor and sensory projections appeared uncrossed in patients with horizontal gaze palsy with progressive scoliosis (HGPPS). In patients affected with HGPPS, we identified mutations in the ROBO3 gene, which shares homology with roundabout genes important in axon guidance in developing Drosophila, zebrafish, and mouse. Like its murine homolog Rig1/Robo3, but unlike other Robo proteins, ROBO3 is required for hindbrain axon midline crossing.

The DNA sequence and comparative analysis of human chromosome 20.

Abstract: Chromosome 5 is one of the largest human chromosomes and contains numerous intrachromosomal duplications, yet it has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding conservation with non-mammalian vertebrates, suggesting that they are functionally constrained. In total, we compiled 177.7 million base pairs of highly accurate finished sequence containing 923 manually curated protein-coding genes including the protocadherin and interleukin gene families. We also completely sequenced versions of the large chromosome-5-specific internal duplications. These duplications are very recent evolutionary events and probably have a mechanistic role in human physiological variation, as deletions in these regions are the cause of debilitating disorders including spinal muscular atrophy.

Combined long and short time-scale X-ray variability of NGC 4051 with RXTE and XMM-Newton

Abstract: We present a comprehensive examination of the X-ray variability of the narrow-line Seyfert 1 (NLS 1) galaxy NGC 405 1, one of the most variable active galactic nuclei (AGN) in the sky. We combine over 6.5 years of frequent monitoring observations by RXTE with a > 100-ks continuous observation by XMM-Newton and so present an overall 2-10 keV power spectral density (PSD) covering an unprecedented frequency range of over 6.5 decades from 10(-2) Hz. The combined RXTE and XMM-Newton PSD is a very good match to the PSD of the galactic black-hole binary system (GBH) Cygnus X-1 when in a 'high', rather than 'low', state, providing the first definite confirmation of an AGN in a 'high' state. We also find that a bending power law, rather than a sharply broken power law, besides being more physical, is a much better description of the high-state PSD of Cygnus X-1 and is also a better description of the PSD of NGC 4051.At low frequencies the PSD of NGC 4051 has a slope of -1.1 bending, at a frequency nu(B) = 8(-3)(+4) x 10(-4) Hz, to a slope Of alpha(H) similar to -2. Although nu(B) does not depend on photon energy, alpha(H) is steeper at lower energies. If nu(B) scales with mass, we imply a black-hole mass of 3(-1)(+2), x 10(5) Mcircle dot in NGC 4051, which is consistent with the recently reported reverberation value of 5(-3)(+6) x 10(5) MCcircle dot. Hence NGC 4051 is emitting at similar to30 per cent L-Edd.NGC 4051 follows the same rms-flux relationship as GBHs, consistent with higher Fourier frequencies being associated with smaller radii.From the cross-power spectra and cross-correlation functions between XMM-Newton light curves in different energy bands, we note that the higher-energy photons lag the lower-energy ones. We also note that the lag is greater for variations of longer Fourier period and increases with the energy separation of the bands. Variations in different wavebands are very coherent at long Fourier periods but the coherence decreases at shorter periods and as the energy separation between bands increases. This behaviour is again similar to that of GBHs, and of MCG-6-30-15, and suggests a radial distribution of frequencies and photon energies with higher energies and higher frequencies being associated with smaller radii.Combining our observations with observations from the literature we find it is not possible to fit all AGN to the same linear scaling of break time-scale with black-hole mass. However, broad-line AGN are consistent with a linear scaling of break time-scale with mass from Cygnus X-1 in its low state and NLS1 galaxies scale better with Cygnus X-1 in its high state. We suggest that the relationship between black-hole mass and break time-scale is a function of at least one other underlying parameter which may be accretion rate or black-hole spin or both.

Effective medium theory of left-handed materials.

Abstract: We analyze the transmission and reflection data obtained through transfer matrix calculations on metamaterials of finite lengths, to determine their effective permittivity $ϵ$ and permeability $\ensuremath{\mu}$. Our study concerns metamaterial structures composed of periodic arrangements of wires, cut wires, split ring resonators (SRRs), closed SRRs, and both wires and SRRs. We find that the SRRs have a strong electric response, equivalent to that of cut wires, which dominates the behavior of left-handed materials (LHM). Analytical expressions for the effective parameters of the different structures are given, which can be used to explain the transmission characteristics of LHMs. Of particular relevance is the criterion introduced by our studies to identify if an experimental transmission peak is left or right handed.

Structure and stability of SiC nanotubes

Abstract: We propose structural and electronic properties of recently synthesized SiC nanotubes. The nanotubes with a Si to C ratio of 1:1 exhibit rich morphologies and are shown to belong to two distinct categories that are close in energies but show significant differences in electronic and transport properties. Similarities and differences are invoked with the case of BN nanotubes to explain the observed surface reconstruction.

Unconventional Magnetism in All-Carbon Nanofoam

Abstract: We report production of nanostructured magnetic carbon foam by a high-repetition-rate, high-power laser ablation of glassy carbon in $\mathrm{Ar}$ atmosphere. A combination of characterization techniques revealed that the system contains both $s{p}^{2}$ and $s{p}^{3}$ bonded carbon atoms. The material is a form of carbon containing graphite-like sheets with hyperbolic curvature, as proposed for ``schwarzite.'' The foam exhibits ferromagnetic-like behavior up to $90\phantom{\rule{0.3em}{0ex}}\mathrm{K}$, with a narrow hysteresis curve and a high saturation magnetization. Such magnetic properties are very unusual for a carbon allotrope. Detailed analysis excludes impurities as the origin of the magnetic signal. We postulate that localized unpaired spins occur because of topological and bonding defects associated with the sheet curvature, and that these spins are stabilized due to the steric protection offered by the convoluted sheets.

The Western and Eastern Roots of the Saami—the Story of Genetic “Outliers” Told by Mitochondrial DNA and Y Chromosomes

Abstract: The Saami are regarded as extreme genetic outliers among European populations. In this study, a high-resolution phylogenetic analysis of Saami genetic heritage was undertaken in a comprehensive context, through use of maternally inherited mitochondrial DNA (mtDNA) and paternally inherited Y-chromosomal variation. DNA variants present in the Saami were compared with those found in Europe and Siberia, through use of both new and previously published data from 445 Saami and 17,096 western Eurasian and Siberian mtDNA samples, as well as 127 Saami and 2,840 western Eurasian and Siberian Y-chromosome samples. It was shown that the "Saami motif" variant of mtDNA haplogroup U5b is present in a large area outside Scandinavia. A detailed phylogeographic analysis of one of the predominant Saami mtDNA haplogroups, U5b1b, which also includes the lineages of the "Saami motif," was undertaken in 31 populations. The results indicate that the origin of U5b1b, as for the other predominant Saami haplogroup, V, is most likely in western, rather than eastern, Europe. Furthermore, an additional haplogroup (H1) spread among the Saami was virtually absent in 781 Samoyed and Ob-Ugric Siberians but was present in western and central European populations. The Y-chromosomal variety in the Saami is also consistent with their European ancestry. It suggests that the large genetic separation of the Saami from other Europeans is best explained by assuming that the Saami are descendants of a narrow, distinctive subset of Europeans. In particular, no evidence of a significant directional gene flow from extant aboriginal Siberian populations into the haploid gene pools of the Saami was found.

Modelling the spectral energy distribution of galaxies. III. Attenuation of stellar light in spiral galaxies

Abstract: We present new calculations of the attenuation of stellar light from spiral galaxies using geometries for stars and dust which can reproduce the entire spectral energy distribution from the ultraviolet (UV) to the Far-infrared (FIR)/submillimeter (submm) and can also account for the surface brightness distribution in both the optical/Near-infrared (NIR) and FIR/submm. The calculations are based on the model of Popescu et al. (2000), which incorporates a dustless stellar bulge, a disk of old stars with associated diffuse dust, a thin disk of young stars with associated diffuse dust, and a clumpy dust component associated with star-forming regions in the thin disk. The attenuations, which incorporate the effects of multiple anisotropic scattering, are derived separately for each stellar component, and presented in the form of easily accessible polynomial fits as a function of inclination, for a grid in optical depth and wavelength. The wavelength range considered is between 912A and 2.2 μm, sampled such that attenuation can be conveniently calculated both for the standard optical bands and for the bands covered by GALEX. The attenuation characteristics of the individual stellar components show marked differences between each other. A general formula is given for the calculation of composite attenuation, valid for any combination of the bulge-to-disk ratio and amount of clumpiness. As an example, we show how the optical depth derived from the variation of attenuation with inclination depends on the bulge-to-disk ratio. Finally, a recipe is given for a self-consistent determination of the optical depth from the Hα/Hβ line ratio.

Improved estimates of cosmological perturbations

Abstract: We recently derived exact solutions for the scalar, vector, and tensor mode functions of a single, minimally coupled scalar plus gravity in an arbitrary homogeneous and isotropic background. These solutions are applied to obtain improved estimates for the primordial scalar and tensor power spectra of anisotropies in the cosmic microwave background.

Color and texture image retrieval using chromaticity histograms and wavelet frames

Abstract: In this paper, we explore image retrieval mechanisms based on a combination of texture and color features. Texture features are extracted using Discrete Wavelet Frames (DWF) analysis, an over-complete decomposition in scale and orientation. Two-dimensional (2-D) or one-dimensional (1-D) histograms of the CIE Lab chromaticity coordinates are used as color features. The 1-D histograms of the a, b coordinates were modeled according to the generalized Gaussian distribution. The similarity measure defined on the feature distribution is based on the Bhattacharya distance. Retrieval benchmarking is performed over the Brodatz album and on images from natural scenes, obtained from the VisTex database of MIT Media Laboratory and from the Corel Photo Gallery. As a performance indicator recall (relative number of correct images retrieved) is measured on both texture and color separately and in combination. Experiments show this approach to be as effective as other methods while computationally more tractable.

Lessons learned from anti-CD40L treatment in systemic lupus erythematosus patients.

Abstract: The CD40-CD40L system has pleiotropic effects in a variety of cells and biological processes including immune response, thrombosis and atherogenesis. Within the immune system, these molecules represent a critical link between its humoral and cellular arms. As a result of these attributes and based on preclinical data in animals, anti-CD40L antibodies were tested in a variety of immunologic diseases including idiopathic thrombocytopenic purpura, psoriasis, Crohn's disease, systemic lupus erythematosus and transplantation. Phase I/II studies in humans with lupus nephritis demonstrated reduction of anti-double-stranded DNA (anti-dsDNA) antibodies but not of protective antibodies. Reduction of anti-DNA was associated with increased serum complement levels and reduced glomerular inflammation. As a result of thrombotic effects, observed even in patients negative for anti-cardiolipin antibodies, there is a temporary halt on further human studies. The reasons for the prothrombotic effects are not clear at present but may represent effects on platelets and/or the endothelium. In view of the significant immunomodulatory effects of anti-CD40L treatment in patients with lupus nephritis, the increasing realization of the importance of premature atherosclerosis in lupus and an increasing amount of data supporting a role for the CD40-CD40L interactions in this process, inhibition of this pathway deserves further exploration in lupus.

Cytochrome P450 pharmacogenetics as a predictor of toxicity and clinical response to pulse cyclophosphamide in lupus nephritis.

Abstract: Objective Pulse cyclophosphamide is the treatment of choice for severe lupus nephritis. However, not all patients respond to this therapy, and gonadal toxicity is of particular concern. Cyclophosphamide is a prodrug that requires activation by cytochrome P450 (CYP) enzymes. We conducted a retrospective cohort study to test whether genetic polymorphisms of these enzymes are associated with the toxicity of, and clinical response to, cyclophosphamide in patients with lupus nephritis. Methods Sixty-two patients with proliferative lupus nephritis treated with cyclophosphamide were genotyped for common variant alleles of CYP2B6, 2C19, 2C9, and 3A5. We examined the association between these genotypes and the following clinical end points: development of premature ovarian failure, end-stage renal disease (ESRD), doubling of serum creatinine level, and achievement of complete renal response. Results The observed frequencies of the variant alleles CYP2B6*5, CYP2C19*2, CYP2C9*2, and CYP3A5*3 were 12.1%, 25.0%, 4.0%, and 75.8%, respectively. Patients who were either heterozygous or homozygous for CYP2C19*2 had a significantly lower risk of developing premature ovarian failure (relative risk 0.10; 95% confidence interval 0.02–0.52), after adjustment for age and total number of cyclophosphamide pulses received. In a survival analysis, patients homozygous for CYP2B6*5 (n = 3) or CYP2C19*2 (n = 4) had a higher probability of reaching ESRD (P = 0.0005) and of doubling the creatinine level (P = 0.0005) as well as a trend toward a lower probability of achieving a complete renal response (P = 0.051). Conclusion Determination of selected cytochrome P450 enzyme genotypes may be valuable for predicting the risk of premature ovarian failure in lupus nephritis patients treated with cyclophosphamide. The association of these genotypes with renal response needs further validation.

Dehydroepiandrosterone and allopregnanolone protect sympathoadrenal medulla cells against apoptosis via antiapoptotic Bcl-2 proteins

Abstract: The neuroactive steroids dehydroepiandrosterone (DHEA), its sulfate ester DHEA sulfate (DHEAS), and allopregnanolone (Allo), produced by the CNS and the adrenals, appear to exert a protective effect in hippocampal and cortical neuron ischemia- and excitotoxicity-induced injury. We hypothesized that they may also play a protective role on the adrenal medulla, an important part of the sympathetic nervous system, and the tissue adjacent to their primary site of production. DHEA, DHEAS, and Allo protected rat chromaffin cells and the rat pheochromocytoma PC12 cell line, an established model for the study of adrenomedullary cell apoptosis and survival, against serum deprivation-induced apoptosis. Their effects were time- and dose-dependent, with EC50 1.8, 1.1, and 1.5 nM, respectively. The antiapoptotic effect of DHEA DHEAS and Allo was compared to that of a long list of structurally related compounds and was found to be structure-specific, confined mainly to conformation 3β-OH-Δ5 for androstenes and 3α-OH for pregnanes. Indeed, 3-keto, Δ4, or C7 hydroxylated androstenes and 3β pregnanes were ineffective. The prosurvival effect of DHEA(S) and Allo was N-methyl-D-aspartate-, GABAA-, sigma1-, or estrogen receptor-independent. It involved the antiapoptotic Bcl-2 proteins, their role being sine qua non for their action because Bcl-2 antisense oligonucleotides reversed their effects. Finally, DHEA(S) and Allo activated cAMP response element-binding protein and NF-κB, upstream effectors of antiapoptotic Bcl-2 protein expression. They also activated the antiapoptotic kinase PKCα/β, a posttranslational activator of Bcl-2 protein. Our findings suggest that decline of DHEA(S) and Allo during aging or stress may leave the adrenal medulla unprotected against proapoptotic challenges.

Experimental observation of true left-handed transmission peaks in metamaterials

Abstract: We report true left-handed (LH) behavior in a composite metamaterial consisting of a periodically arranged split ring resonator (SRR) and wire structures. We demonstrate the magnetic resonance of the SRR structure by comparing the transmission spectra of SRRs with those of closed SRRs. We have confirmed experimentally that the effective plasma frequency of the LH material composed of SRRs and wires is lower than the plasma frequency of the wires. A well-defined LH transmission band with a peak value of -1.2 dB (-0.3 dB/cm) was obtained. The experimental results agree extremely well with the theoretical calculations.

Heads or tails: host-parasite interactions in the Drosophila-Wolbachia system.

Abstract: Wolbachia strains are endosymbiotic bacteria typically found in the reproductive tracts of arthropods. These bacteria manipulate host reproduction to ensure maternal transmission. They are usually transmitted vertically, so it has been predicted that they have evolved a mechanism to target the host's germ cells during development. Through cytological analysis we found that Wolbachia strains display various affinities for the germ line of Drosophila. Different Wolbachia strains show posterior, anterior, or cortical localization in Drosophila embryos, and this localization is congruent with the classification of the organisms based on the wsp (Wolbachia surface protein) gene sequence. This embryonic distribution pattern is established during early oogenesis and does not change until late stages of embryogenesis. The posterior and anterior localization of Wolbachia resembles that of oskar and bicoid mRNAs, respectively, which define the anterior-posterior axis in the Drosophila oocyte. By comparing the properties of a single Wolbachia strain in different host backgrounds and the properties of different Wolbachia strains in the same host background, we concluded that bacterial factors determine distribution, while bacterial density seems to be limited by the host. Possible implications concerning cytoplasmic incompatibility and evolution of strains are discussed.

Conserved features of type III secretion.

Abstract: Type III secretion systems (TTSSs) are essential mediators of the interaction of many Gram-negative bacteria with human, animal or plant hosts. Extensive sequence and functional similarities exist between components of TTSS from bacteria as diverse as animal and plant pathogens. Recent crystal structure determinations of TTSS proteins reveal extensive structural homologies and novel structural motifs and provide a basis on which protein interaction networks start to be drawn within the TTSSs, that are consistent with and help rationalize genetic and biochemical data. Such studies, along with electron microscopy, also established common architectural design and function among the TTSSs of plant and mammalian pathogens, as well as between the TTSS injectisome and the flagellum. Recent comparative genomic analysis, bioinformatic genome mining and genome-wide functional screening have revealed an unsuspected number of newly discovered effectors, especially in plant pathogens and uncovered a wider distribution of TTSS in pathogenic, symbiotic and commensal bacteria. Functional proteomics and analysis further reveals common themes in TTSS effector functions across phylogenetic host and pathogen boundaries. Based on advances in TTSS biology, new diagnostics, crop protection and drug development applications, as well as new cell biology research tools are beginning to emerge.

Generation of transgenic potato plants highly resistant to potato virus Y (PVY) through RNA silencing

Abstract: In this study we applied RNA silencing to engineer potato plants that are resistant to potato virus Y (PVY). We expressed double-stranded (ds) RNA derived from the 3′ terminal part of the coat protein gene of PVY, which is highly conserved in sequence amongst different PVY isolates, in transgenic potatoes of the commercial variety ‘Spunta’. Transgenic plants were analyzed for generation of transgene-derived short interfering RNAs (siRNAs) prior to virus inoculation. Twelve of fifteen transgenic lines produced siRNAs and were highly resistant to three strains of PVY, each belonging to three different subtypes of the virus (PVYN, PVYO and PVYNTN). Infection of transgenic plants with Potato virus X (PVX) simultaneously or prior to the challenge with PVY did not interfere with PVY-resistance.

The WEBT BL Lacertae Campaign 2001 and its extension. Optical light curves and colour analysis 1994-2002

Abstract: BL Lacertae has been the target of four observing campaigns by the Whole Earth Blazar Telescope (WEBT) collaboration. In this paper we present UBVRI light curves obtained by the WEBT from 1994 to 2002, including the last, extended BL Lac 2001 campaign. A total of about 7500 optical observations performed by 31 telescopes from Japan to Mexico have been collected, to be added to the similar to 15 600 observations of the BL Lac Campaign 2000. All these data allow one to follow the source optical emission behaviour with unprecedented detail. The analysis of the colour indices reveals that the flux variability can be interpreted in terms of two components: longer-term variations occurring on a few-day time scale appear as mildly-chromatic events, while a strong bluer-when-brighter chromatism characterizes very fast (intraday) flares. By decoupling the two components, we quantify the degree of chromatism inferring that longer-term flux changes imply moving along a similar to0.1 bluer-when-brighter slope in the B-R versus R plane; a steeper slope of similar to0.4 would distinguish the shorter-term variations. This means that, when considering the long-term trend, the B-band flux level is related to the R-band one according to a power law of index similar to1.1. Doppler factor variations on a "convex" spectrum could be the mechanism accounting for both the long-term variations and their slight chromatism.