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Nuclear Regions (nuclear + regions)
Selected AbstractsSpatial analysis of taxonomic and genetic patterns and their potential for understanding evolutionary historiesJOURNAL OF BIOGEOGRAPHY, Issue 11 2004Sophia A. Bickford Abstract Aim, The aim of this research is to develop and investigate methods for the spatial analysis of diversity based on genetic and taxonomic units of difference. We use monophyletic groups of species to assess the potential for these diversity indices to elucidate the geographical components of macro-scaled evolutionary processes. Location, The range occupied by Pultenaea species in temperate and sub-tropical eastern Australia, extending from western South Australia (133° E,32° S) to Tasmania (146° E,43° S) to coastal central Queensland (148° E,20° S). Methods, We applied a series of both spatially explicit and spatially implicit analyses to explore the nature of diversity patterns in the genus Pultenaea, Fabaceae. We first analysed the eastern species as a whole and then the phylogenetic groups within them. We delineated patterns of endemism and biotic (taxon) regions that have been traditionally circumscribed in biogeographical studies of taxa. Centres of endemism were calculated using corrected weighted endemism at a range of spatial scales. Biotic regions were defined by comparing the similarity of species assemblages of grid cells using the Jaccard index and clustering similar cells using hierarchical clustering. On the basis that genetically coherent areas were likely to be more evolutionary informative than species patterns, genetic indices of similarity and difference were derived. A matrix of similarity distances between taxa was generated based on the number of shared informative characters of two sections of trnL-F and ndhF chloroplast nuclear regions. To identify genetically similar areas, we clustered cells using the mean genetic similarities of the species contained within each pair of cells. Measures of the mean genetic similarity of species in areas were delineated using a geographically local multi-scalar approach. Resultant patterns of genetic diversity are interpreted in relation to theories of the evolutionary relationships between species and species groups. Results, Centres of Pultenaea endemism were defined, those of clades 1 congruent with the spatially separated centres of clades 2 and 3. The taxonomic classification analysis defined cells with shared groups of species, which in some cases clustered when plotted in geographic space, defining biotic regions. In some instances the distribution of biotic regions was congruent with centres of endemism, however larger scale groupings were also apparent. In clade 1 one set of species was replaced by another along the extent of the range, with some connectivity between some geographically disjunct regions due to the presence of widespread species. In the combined analysis of clade 2 and 3 species the major biotic (taxonomic) groups with geographic coherence were defined by species in the respective clades, representing the geographic separation of these clades. However distinctive biotic regions within these main groupings of clades 2 and 3 were also apparent. Clustering cells using the mean genetic similarities of the species contained within each pair of cells indicated that some of the taxonomically defined biotic boundaries were the result of changes in composition of closely related species. This was most apparent in clades 1 and 2 where most cells were highly genetically similar. In clade 3 genetically distinct groups remained and were in part defined by sister taxa with disjunct distributions. Gradients in mean genetic similarity became more apparent from small to larger scales of analysis. At larger scales of analysis, regions of different levels of genetic diversity were delineated. Regions with highest diversity levels (lowest level of similarity) often represented regions where the ranges of phylogenetically distinctive species intergraded. Main conclusions, The combined analysis of diversity, phylogeny and geography has potential to reveal macro-scaled evolutionary patterns from which evolutionary processes may be inferred. The spatial genetic diversity indices developed in this study contribute new methods for identifying coherent evolutionary units in the landscape, which overcome some of the limitations of using taxonomic data, and from which the role of geography in evolutionary processes can be tested. We also conclude that a multiple-index approach to diversity pattern analysis is useful, especially where patterns may be the result of a long history of different environmental changes and related evolutionary events. The analysis contributes to the knowledge of large-scale diversity patterns of Pultenaea which has relevance for the assessment of the conservation status of the genus. [source] Electron microscopic findings in non-alcoholic fatty liver disease: Is there a difference between hepatosteatosis and steatohepatitis?JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, Issue 3 2010Emel Ahishali Abstract Background and Aims:, Non-alcoholic fatty liver disease has long been accepted as benign; however, recent evidence suggests that the disease may progress to cirrhosis and hepatocellular carcinoma, although the natural course of the disease is still unclear. This study was designed to comparatively evaluate electron microscopic features of non-alcoholic fatty liver (NAFL) and non-alcoholic steatohepatitis (NASH). Methods:, Quantitative and semi-quantitative ultrastructural evaluations were performed on liver biopsies from 23 patients, 10 with NAFL and 13 with NASH. Results:, No statistically significant difference was noted between NAFL and NASH patients in ultrastructural features of hepatocytes including megamitochondria, intramitochondrial crystalline inclusions, mitochondrial matrix granules, foamy cytoplasmic appearance, electron-lucent and glycogen-containing nuclear regions, lipofuscin granules, or an increased frequency of vesicles containing electron-dense material in peribiliary Golgi zone; however, the mitochondrial diameter was significantly higher in the NASH patients. Intercellular distance and microvilli between hepatocytes, collagen and electron-dense material accumulation in the space of Disse, electron-dense material accumulation and microvillus density in bile canaliculi did not differ significantly between the groups. Conclusions:, Our data show that, although NAFL and NASH can be distinguished by their distinct light microscopic features, ultrastructural characteristics are similar, which suggests that NAFL may also have the potential to progress to fibrosis and cirrhosis like NASH. [source] Testing candidate plant barcode regions in the MyristicaceaeMOLECULAR ECOLOGY RESOURCES, Issue 3 2008S. G. NEWMASTER Abstract The concept and practice of DNA barcoding have been designed as a system to facilitate species identification and recognition. The primary challenge for barcoding plants has been to identify a suitable region on which to focus the effort. The slow relative nucleotide substitution rates of plant mitochondria and the technical issues with the use of nuclear regions have focused attention on several proposed regions in the plastid genome. One of the challenges for barcoding is to discriminate closely related or recently evolved species. The Myristicaceae, or nutmeg family, is an older group within the angiosperms that contains some recently evolved species providing a challenging test for barcoding plants. The goal of this study is to determine the relative utility of six coding (Universal Plastid Amplicon , UPA, rpoB, rpoc1, accD, rbcL, matK) and one noncoding (trnH-psbA) chloroplast loci for barcoding in the genus Compsoneura using both single region and multiregion approaches. Five of the regions we tested were predominantly invariant across species (UPA, rpoB, rpoC1, accD, rbcL). Two of the regions (matK and trnH-psbA) had significant variation and show promise for barcoding in nutmegs. We demonstrate that a two-gene approach utilizing a moderately variable region (matK) and a more variable region (trnH-psbA) provides resolution among all the Compsonuera species we sampled including the recently evolved C. sprucei and C. mexicana. Our classification analyses based on nonmetric multidimensional scaling ordination, suggest that the use of two regions results in a decreased range of intraspecific variation relative to the distribution of interspecific divergence with 95% of the samples correctly identified in a sequence identification analysis. [source] Dynamic distribution of BIMGPP1 in living hyphae of Aspergillus indicates a novel role in septum formationMOLECULAR MICROBIOLOGY, Issue 5 2002H. Fox Summary Mutation of bimG, the major protein phosphatase 1 gene in Aspergillus nidulans, causes multiple cell cycle and hyphal growth defects that are associated with overphosphorylation of subcellular components. We have used functional translational fusions with the green fluorescent protein (GFP) to show that BIMG has at least four discrete locations within growing hyphae. Three of these locations, the hyphal tip, the spindle pole body and the nucleus, correlate with previously known requirements for bimGPP1 in mitosis and hyphal growth and are highly dynamic. BIMG-GFP in the hyphal tip seemed to be associated with the plasma membrane and formed a collar of fluorescence within the apical dome. The distribution of nuclear BIMG-GFP varied depending on nutritional conditions; on poor medium, it concentrated more in the nucleolus than in the nucleoplasm, whereas on rich medium, it was more evenly distributed between the two nuclear regions. The association of BIMG-GFP with developing septa was transient, and we present evidence that BIMG phosphatase plays a direct role in septum formation, distinct from its role in mitosis. We conclude that, by being physically present at several sites, the BIMG phosphatase has roles in multiple cellular processes. [source] The properties of the stellar populations in ULIRGs , I. Sample, data and spectral synthesis modellingMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 3 2009J. Rodríguez Zaurín ABSTRACT We present deep long-slit optical spectra for a sample of 36 ultraluminous infrared galaxies (ULIRGs), taken with the William Herschel Telescope on La Palma with the aim of investigating the star formation histories and testing evolutionary scenarios for such objects. Here we present the sample, the analysis techniques and a general overview of the properties of the stellar populations; a more detailed discussion will be presented in a forthcoming paper. Spectral synthesis modelling has been used in order to estimate the ages of the stellar populations found in the diffuse light sampled by the spectra in both the nuclear and extended regions of the target galaxies. We find that adequate fits can be obtained using combinations of young stellar populations (YSPs; tYSP, 2 Gyr), with ages divided into two groups: very young stellar populations (VYSPs; tVYSP, 100 Myr) and intermediate-young stellar populations (IYSPs; 0.1 < tIYSP, 2 Gyr). Our results show that YSPs are present at all locations of the galaxies covered by our slit positions, with the exception of the northern nuclear region of the ULIRG IRAS 23327+2913. Furthermore, VYSPs are present in at least 85 per cent of the 133 extraction apertures used for this study, being more significant in the nuclear regions of the galaxies. Old stellar populations (OSPs; tOSP > 2 Gyr) do not make a major contribution to the optical light in the majority of the apertures extracted. In fact they are essential for fitting the spectra in only 5 per cent (seven) of the extracted apertures. The estimated total masses for the YSPs (VYSPs + IYSPs) are in the range 0.18 × 1010,MYSP, 50 × 1010 M,. We have also estimated the bolometric luminosities associated with the stellar populations detected at optical wavelengths, finding that they fall in the range 0.07 × 1012 < Lbol < 2.2 × 1012 L,. In addition, we find that reddening is significant at all locations in the galaxies. This result emphasizes the importance of accounting for reddening effects when modelling the stellar populations of star-forming galaxies. [source] The ionization of the emission-line gas in young radio galaxiesMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 2 2009J. Holt ABSTRACT This paper is the second in a series in which we present intermediate-resolution, wide-wavelength coverage spectra for a complete sample of 14 compact radio sources, taken with the aim of investigating the impact of the nuclear activity on the circumnuclear interstellar medium (ISM) in the early stages of radio source evolution. In the first paper (Holt, Tadhunter & Morganti), we presented the kinematic results from the nuclear emission-line modelling and reported fast outflows in the circumnuclear gas. In this paper, we use the line fluxes to investigate the physical conditions and dominant ionization mechanisms of the emission-line gas. We find evidence for large electron densities and high reddening in the nuclear regions, particularly in the broader, blueshifted components. These results are consistent with the idea that the young, recently triggered radio sources still reside in dense and dusty cocoons deposited by the recent activity triggering event (merger/interaction). In addition, we find that the quiescent nuclear and extended narrow components are consistent with active galactic nucleus (AGN) photoionization, split between simple-slab AGN photoionization and mixed-medium photoionization models. For the nuclear broader and shifted components, the results are less clear. Whilst there are suggestions that the broader components may be closer to shock plus precursor models on the diagnostic diagrams, and that the electron temperatures and densities are high, we are unable to unambiguously distinguish the dominant ionization mechanism using the optical emission-line ratios. This is surprising given the strong evidence for jet,cloud interactions (broad emission lines, large outflow velocities and strong radio-optical alignments), which favours the idea that the warm gas has been accelerated in shocks driven by the radio lobes expanding through a dense cocoon of gas deposited during the triggering event. [source] Multiwavelength study of the nuclei of a volume-limited sample of galaxies , II.MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 4 2007Optical, infrared, radio observations ABSTRACT We present optical and infrared broad-band images, radio maps, and optical spectroscopy for the nuclear region of a sample of nearby galaxies. The galaxies have been drawn from a complete volume-limited sample for which we have already presented X-ray imaging. We modelled the stellar component of the spectroscopic observations to determine the star formation history of our targets. Diagnostic diagrams were used to classify the emission-line spectra and determine the ionizing mechanism driving the nuclear regions. All those sources classified as active galactic nuclei present small Eddington ratios (,10,3,10,6), implying a very slow growth rate of their black holes. We finally investigate the relative numbers of active and normal nuclei as a function of host galaxy luminosity and find that the fraction of active galaxies slowly rises as a function of host absolute magnitude in the MB,,12 to ,22 range. [source] A census of young stellar populations in the warm ULIRG PKS 1345+12MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 4 2007J. Rodríguez Zaurín ABSTRACT We present a detailed investigation of the young stellar populations (YSP) in the radio-loud ultraluminous infrared galaxy (ULIRG), PKS 1345+12 (z= 0.12), based on high-resolution Hubble Space Telescope (HST) imaging and long-slit spectra taken with the William Herschel Telescope (WHT) at La Palma. While the images clearly show bright knots suggestive of super star clusters (SSCs), the spectra reveal the presence of YSP in the diffuse light across the full extent of the halo of the merging double nucleus system. Spectral synthesis modelling has been used to estimate the ages of the YSP for both the SSC and the diffuse light sampled by the spectra. For the SSC, we find ages tSSC < 6 Myr with reddenings 0.2 < E(B,V) < 0.5 and masses 106 < MYSPSSC < 107 M,. In the region to the south of the western nucleus that contains the SSC our modelling of the spectrum of the diffuse light is also consistent with a relatively young age for the YSP (,5 Myr), although older YSP ages cannot be ruled out. However, in other regions of the galaxy we find that the spectra of the diffuse light component can only be modelled with a relatively old post-starburst YSP (0.04,1.0 Gyr) or with a disc galaxy template spectrum. The results demonstrate the importance of accounting for reddening in photometric studies of SSC and highlight the dangers of focusing on the highest surface brightness regions when trying to obtain a general impression of the star formation activity in the host galaxies of ULIRGs. The case of PKS 1345+12 provides clear evidence that the star formation histories of the YSP in ULIRGs are complex. While the SSC represent the vigorous phase of star formation associated with the final stages of the merger, the YSP in the diffuse light are likely to represent star formation in one or more of the merging galaxies at an earlier stage or prior to the start of the merger. Intriguingly, our long-slit spectra show line splitting at the locations of the SSC, indicating that they are moving at up to 450 km s,1 with respect to the local ambient gas. Given their kinematics, it is plausible that the SSCs have been formed either in fast moving gas streams/tidal tails that are falling back into the nuclear regions as part of the merger process or as a consequence of jet-induced star formation linked to the extended, diffuse radio emission detected in the halo of the galaxy. [source] The 1,1000 ,m spectral energy distributions of far-infrared galaxiesMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 2 2006A. Sajina ABSTRACT Galaxies selected at 170 ,m by the Infrared Space Observatory (ISO) Far-IR BACKground (FIRBACK) survey represent the brightest ,10 per cent of the cosmic infrared background. Examining their nature in detail is therefore crucial for constraining models of galaxy evolution. Here, we combine Spitzer archival data with previous near-infrared (near-IR), far-IR, and submillimetre (submm) observations of a representative sample of 22 FIRBACK galaxies spanning three orders of magnitude in IR luminosity. We fit a flexible, multicomponent, empirical SED model of star-forming galaxies designed to model the entire ,1,1000 ,m wavelength range. The fits are performed with a Markov Chain Monte Carlo (MCMC) approach, allowing for meaningful uncertainties to be derived. This approach also highlights degeneracies such as between Td and ,, which we discuss in detail. From these fits and standard relations we derive: LIR, LPAH, star formation rate (SFR), ,V, M*, Mdust, Td, and ,. We look at a variety of correlations between these and combinations thereof in order to examine the physical nature of these galaxies. Our conclusions are supplemented by morphological examination of the sources, and comparison with local samples. We find the bulk of our sample to be consistent with fairly standard size and mass disc galaxies with somewhat enhanced star formation relative to local spirals, but likely not bona fide starbursts. A few higher- z luminous infrared galaxies (LIGs) and ultraluminous infrared galaxies (ULIGs) are also present, but contrary to expectation, they are weak mid-IR emitters and overall are consistent with star formation over an extended cold region rather than concentrated in the nuclear regions. We discuss the implications of this study for understanding populations detected at other wavelengths, such as the bright 850-,m Submillimetre Common-User Bolometer Array (SCUBA) sources or the faint Spitzer 24-,m sources. [source] NtSET1, a member of a newly identified subgroup of plant SET-domain-containing proteins, is chromatin-associated and its ectopic overexpression inhibits tobacco plant growthTHE PLANT JOURNAL, Issue 4 2001Wen-Hui Shen Summary The SET- and chromo-domains are recognized as signature motifs for proteins that contribute to epigenetic control of gene expression through effects on the regional organization of chromatin structure. This paper reports the identification of a novel subgroup of SET-domain-containing proteins in tobacco and Arabidopsis, which show highest homologies with the Drosophila position-effect-variegation repressor protein SU(VAR)3,9 and the yeast centromer silencing protein CLR4. The tobacco SET-domain-containing protein (NtSET1) was fused to the green fluorescence protein (GFP) that serves as a visual marker for localization of the recombinant protein in living cells. Whereas control GFP protein alone was uniformly dispersed within the nucleus and cytoplasm, the NtSET1-GFP fusion protein showed a non-uniform localization to multiple nuclear regions in interphase tobacco TBY2 cells. During mitosis, the NtSET1-GFP associated with condensed chromosomes with a non-random distribution. The NtSET1 thus appears to have distinct target regions in the plant chromatin. Overexpression of the NtSET1-GFP in transgenic tobacco inhibited plant growth, implicating the possible involvement of the NtSET1 in transcriptional repression of growth control genes through the formation of higher-order chromatin domains. [source] | ||||||||||