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Distinct Differences (distinct + difference)
Selected AbstractsCombined bromodeoxyuridine immunocapture and terminal-restriction fragment length polymorphism analysis highlights differences in the active soil bacterial metagenome due to Glomus mosseae inoculation or plant speciesENVIRONMENTAL MICROBIOLOGY, Issue 12 2005Veronica Artursson Summary High numbers of bacteria are associated with arbuscular mycorrhizal (AM) fungi, but their functions and in situ activities are largely unknown and most have never been characterized. The aim of the present study was to study the impact of Glomus mosseae inoculation and plant type on the active bacterial communities in soil by using a molecular approach, bromodeoxyuridine (BrdU) immunocapture in combination with terminal-restriction fragment length polymorphism (T-RFLP). This approach combined with sequence information from clone libraries, enabled the identification of actively growing populations, within the total bacterial community. Distinct differences in active bacterial community compositions were found according to G. mosseae inoculation, treatment with an antifungal compound (Benomyl) and plant type. The putative identities of the dominant bacterial species that were activated as a result of G. mosseae inoculation were found to be mostly uncultured bacteria and Paenibacillus species. These populations may represent novel bacterial groups that are able to influence the AM relationship and its subsequent effect on plant growth. [source] Improving thermostability and catalytic activity of pyranose 2-oxidase from Trametes multicolor by rational and semi-rational designFEBS JOURNAL, Issue 3 2009Oliver Spadiut The fungal homotetrameric flavoprotein pyranose 2-oxidase (P2Ox; EC 1.1.3.10) catalyses the oxidation of various sugars at position C2, while, concomitantly, electrons are transferred to oxygen as well as to alternative electron acceptors (e.g. oxidized ferrocenes). These properties make P2Ox an interesting enzyme for various biotechnological applications. Random mutagenesis has previously been used to identify variant E542K, which shows increased thermostability. In the present study, we selected position Leu537 for saturation mutagenesis, and identified variants L537G and L537W, which are characterized by a higher stability and improved catalytic properties. We report detailed studies on both thermodynamic and kinetic stability, as well as the kinetic properties of the mutational variants E542K, E542R, L537G and L537W, and the respective double mutants (L537G/E542K, L537G/E542R, L537W/E542K and L537W/E542R). The selected substitutions at positions Leu537 and Glu542 increase the melting temperature by approximately 10 and 14 °C, respectively, relative to the wild-type enzyme. Although both wild-type and single mutants showed first-order inactivation kinetics, thermal unfolding and inactivation was more complex for the double mutants, showing two distinct phases, as revealed by microcalorimetry and CD spectroscopy. Structural information on the variants does not provide a definitive answer with respect to the stabilizing effects or the alteration of the unfolding process. Distinct differences, however, are observed for the P2Ox Leu537 variants at the interfaces between the subunits, which results in tighter association. [source] Ciliate biogeography in Antarctic and Arctic freshwater ecosystems: endemism or global distribution of species?FEMS MICROBIOLOGY ECOLOGY, Issue 2 2007Wolfgang Petz Abstract Ciliate diversity was investigated in situ in freshwater ecosystems of the maritime (South Shetland Islands, mainly Livingston Island, 63°S) and continental Antarctic (Victoria Land, 75°S), and the High Arctic (Svalbard, 79°N). In total, 334 species from 117 genera were identified in both polar regions, i.e. 210 spp. (98 genera) in the Arctic, 120 spp. (73 genera) in the maritime and 59 spp. (41 genera) in the continental Antarctic. Forty-four species (13% of all species) were common to both Arctic and Antarctic freshwater bodies and 19 spp. to both Antarctic areas (12% of all species). Many taxa are cosmopolitans but some, e.g. Stentor and Metopus spp., are not, and over 20% of the taxa found in any one of the three areas are new to science. Cluster analysis revealed that species similarity between different biotopes (soil, moss) within a study area was higher than between similar biotopes in different regions. Distinct differences in the species composition of freshwater and terrestrial communities indicate that most limnetic ciliates are not ubiquitously distributed. These observations and the low congruence in species composition between both polar areas, within Antarctica and between high- and temperate-latitude water bodies, respectively, suggest that long-distance dispersal of limnetic ciliates is restricted and that some species have a limited geographical distribution. [source] Identification of Atlantic bluefin tuna (Thunnus thynnus) stocks from putative nurseries using otolith chemistryFISHERIES OCEANOGRAPHY, Issue 2 2003Jay R. Rooker Abstract Chemical signatures in the otoliths of teleost fishes represent natural tags that may reflect differences in the chemical and physical characteristics of an individuals' environment. Otolith chemistry of Atlantic bluefin tuna (Thunnus thynnus) was quantified to assess the feasibility of using these natural tags to discriminate juveniles (age 0 and age 1) from putative nurseries. A suite of six elements (Li, Mg, Ca, Mn, Sr and Ba) was measured in whole otoliths using solution-based inductively coupled plasma mass spectrometry. Otolith chemistry of age-1 T. thynnus collected from the two primary nurseries in the Mediterranean Sea and western Atlantic Ocean differed significantly, with a cross-validated classification accuracy of 85%. Spatial and temporal variation in otolith chemistry was evaluated for age-0 T. thynnus collected from three nurseries within the Mediterranean Sea: Alboran Sea (Spain), Ligurian Sea (northern Italy), and Tyrrhenian Sea (southern Italy). Distinct differences in otolith chemistry were detected among Mediterranean nurseries and classification accuracies ranged from 62 to 80%. Interannual trends in otolith chemistry were observed between year classes of age-0 T. thynnus in the Alboran Sea; however, no differences were detected between year classes in the Tyrrhenian Sea. Age-0 and age-1 T. thynnus collected from the same region (Ligurian Sea) were also compared and distinct differences in otolith chemistry were observed, indicating ontogenetic shifts in habitat or elemental discrimination. Findings suggest that otolith chemistry of juvenile T. thynnus from different nurseries are distinct and chemical signatures show some degree of temporal persistence, indicating the technique has considerable potential for use in future assessments of population connectivity and stock structure of T. thynnus. [source] Grazing impact and phenology of the freshwater sponge Ephydatia muelleri and the bryozoans Plumatella emarginata and Fredericella sultana under experimental warmingFRESHWATER BIOLOGY, Issue 5 2009ANDREAS VOHMANN Summary 1.,Both the clearance rates (CR) and abundances of the freshwater sponge Ephydatia muelleri and the bryozoans Plumatella emarginata and Fredericella sultana were investigated from autumn to spring under different temperature regimes. The experiments were performed in bypass channels of the River Rhine (Cologne, Germany) in which temperature could be manipulated. 2.,The impact of temperature increase on CRs depends upon the grazer: E. muelleri showed a clear increase in CRs with increasing temperature whereas P. emarginata was not significantly affected by experimental warming. 3.,Distinct differences in food preference were found for the sponge (which is an efficient grazer of bacteria and small algae) and for the bryozoan P. emarginata (which feeds primarily on large algae, and with no significant grazing on bacteria). 4.,In contrast to their temperature-related patterns in CR, respiration of both P. emarginata and E. muelleri increased with temperature between 19 and 32 °C, suggesting that the risk of experiencing energy deficiency at high temperatures due to increased metabolic rates is particularly high for the bryozoan. 5.,A temperature elevation of 3 °C above the natural Rhine temperature resulted in a delay in the disappearance of active tissue and formation of resting stages for E. muelleri in autumn. This delay ranged from 8 (beginning of gemmulation) to 22 days (termination of gemmulation). In contrast, there was no distinct effect of warming on the disappearance of active zooids of the two bryozoan species in autumn. However, warming can positively affect the maintenance of active zooids during winter in F. sultana. In spring, the appearance of active zooids of P. emarginata was clearly stimulated by temperature elevations, whereas the hatching of both F. sultana and E. muelleri was hardly affected by warming. 6.,The study demonstrated different patterns in the thermal ecology of the two freshwater bryozoans and the sponge in comparison to other filter feeders, particularly mussels. Such patterns need to be considered when predicting the impact of temperature on pelagic-benthic coupling in aquatic habitats. [source] Characteristics of Ralstonia solanacearum Biovar N2 Strains in AsiaJOURNAL OF PHYTOPATHOLOGY, Issue 4 2005M. Horita Abstract Ralstonia solanacearum biovar N2 strains isolated in Asia were compared by biochemical tests with biovar N2 strains from South America and biovar 2 (race 3) strains from Africa, America, Asia and Europe. Distinct differences were found between Asian and South American strains of biovar N2, and between Asian biovar N2 and biovar 2 strains with respect to their ability to utilize several carbon sources. Using cluster analysis based on repetitive sequence-based polymerase chain reaction (rep-PCR) genomic fingerprints, the Asian biovar N2 strains were divided into two groups, group 1 containing Japanese strains and group 2 containing Indonesian and Philippine strains. The fingerprints showed the genetic diversity of biovar N2 strains in Asia. [source] Microbial Baeyer,Villiger Oxidation of Prochiral Polysubstituted Cyclohexanones by Recombinant Whole-Cells Expressing Two Bacterial MonooxygenasesEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 5 2005Marko D. Mihovilovic Abstract The microbial Baeyer,Villiger oxidation of prochiral 3,5-dimethylcyclohexanones bearing various functionalities with recombinant E. coli cells overexpressing cyclohexanone monooxygenase from Acinetobacter sp. NCIMB 9871 and cyclopentanone monooxygenase from Comamonas sp. NCIMB 9872 has been investigated. A distinct difference in substrate specificity and stereoselectivity of the two enzymes was observed, and enantiocomplementary products were obtained in some cases. The biocatalytic systems enabled access to chiral lactones as valuable intermediates for the total synthesis of various natural compounds. Substituents with varying lipophilicity and hybridization have been prepared by a diastereoselective synthetic route and subsequently bio-transformed for the investigation of conformational and electronic effects on the biooxidation,. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Sorption of phosphorus in field-moist and air-dried samples from four weakly developed cultivated soil profilesEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 1 2007T. PeltovuoriArticle first published online: 9 FEB 200 Summary Sorption of phosphorus (P) in complete soil profiles in northern Europe is not adequately documented. I measured the sorption in genetic horizons of four cultivated soils (Inceptisols, Spodosol) in Finland using both field-moist and air-dried soil samples, fitted modified Freundlich equations (Q = a × Ib , q) to the data, and presented the results in quantity/intensity (Q/I) graphs. Least-squares-estimates for the parameters of the modified Freundlich equation (a, b, q) were found to be imprecise measures of sorption. Values derived from the fitted equations (the amount of P sorbed at the P concentration of 2 mg litre,1 and P buffering capacity at the same concentration) were more precise. Both were correlated with concentrations of oxalate-extractable iron and aluminium. In all soils, there was a distinct difference in sorption between the fertilized Ap horizons and the subsurface horizons, which retained P strongly. Most of the sorption capacity was located in the B horizons at depths between 0.3 and 0.7 m. The results demonstrate the effects of soil-forming processes and human impact on the sorption of P in the soils. Drying the samples prior to the sorption experiments altered the shape of the Q/I graphs. It increased dissolution of P at small P concentrations, sorption at large P concentrations, and the estimates for P buffering capacity. The effects of drying soil samples on the results and the imprecision of the parameters estimated with the modified Freundlich equation should be taken into account when interpreting results of Q/I experiments. [source] Connecting Atmosphere and Wetland: Energy and Water Vapour ExchangeGEOGRAPHY COMPASS (ELECTRONIC), Issue 4 2008Peter M. Lafleur Wetlands are ubiquitous over the globe, comprise a vast array of ecosystem types and are of great ecological and social importance. Their functioning is intimately tied to the atmosphere by the energy and mass exchanges that take place across the wetland,atmosphere boundary. This article examines recent research into these exchanges, with an emphasis on the water vapour exchange. Although broad classes of wetland type, such as fen, bog and marsh, can be defined using ecological or hydrologic metrics, distinct difference in energy exchanges between the classes cannot be found. This arises because there are many factors that control the energy exchanges and interplay of these factors is unique to every wetland ecosystem. Wetlands are more similar in their radiation balances than in the partitioning of this energy into conductive and turbulent heat fluxes. This is especially true of evapotranspiration (ET) rates, which vary considerably among and within wetland classes. A global survey of wetland ET studies shows that location has little to do with ET rates and that variation in rates is largely determined by local climate and wetland characteristics. Recent modelling studies suggest that although wetlands occupy a small portion of the global land surface, their water and energy exchanges may be important in regional and global climates. Although the number of studies of wetland,atmosphere interactions has increased in recent years more research is needed. Five key areas of study are identified: (i) the importance of moss covers, (ii) lack of study in tropical systems, (iii) inclusion of wetlands in global climate models, (iv) importance of microforms in wetlands and their scaling to the whole ecosystem, and (v) the paucity of annual ET measurements. [source] A numerical estimation of the effects of a cylindrical hole and imperfect bonding on stability of a fibre in an elastic matrixINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 6 2001Yuri N. Lapusta Abstract A simple numerical model based on three-dimensional analytical considerations is proposed for an estimation of the local effects of a cylindrical hole in the matrix as well as of fibre,matrix interface imperfections on compressive stability of fibres in fibre-reinforced composites. The geometry of the model includes an inclusion (a fibre) in a matrix with the assumption of an imperfect bonding at the interface and a cylindrical hole in the closest neighbourhood. Then the problem formulation is idealized in two directions, providing a possibility of establishing lower and upper bounds for critical loads for the case of a matrix with a cylindrical hole of a non-circular cross-section as well as for the case of interface imperfections with the possibility of sliding without discontinuity of the displacements normal to the interface. The model takes into account the distinct difference in the properties of the fibre and the matrix and the spatial character of the problem at the microlevel. It is based on individual consideration of the fibre and the matrix with a hole with the necessity of satisfying certain idealized bonding conditions between them. Copyright © 2001 John Wiley & Sons, Ltd. [source] A synoptic-scale climate analysis of anomalous snow water equivalent over the Northern Great Plains of the USAINTERNATIONAL JOURNAL OF CLIMATOLOGY, Issue 8 2003Andrew Grundstein Abstract The Northern Great Plains is a region where variations in seasonal snow accumulation can have a dramatic affect on regional hydrology. In the past, one of the problems in studying snow hydrology has been obtaining information of sufficiently high temporal and spatial resolution on the water content of the snowpack. This project used a hybrid climatology of snow water equivalent (SWE) that incorporated both model and observed data. This climatology has a long time series (49 years) and a high spatial resolution (1° × 1°) sufficient for use in a climatic analysis. The long and complete time series of SWE generated in this project allowed for a comprehensive analysis of the meteorological and climate forcing mechanisms that influence the amount of SWE. The five largest (high SWE) and five smallest SWE (low SWE) accumulations on 1 March were examined. High SWE years received greater snowfall and fewer accumulated melting degree days throughout the season. Large SWE accumulations at the end of the season, however, were not always associated with deep snowpacks early in the season. Also, all five high SWE years had above normal snowfall in February. Years with small or no SWE had below-average snowfall but greater than average accumulated melting degree days. A synoptic analysis examined both atmospheric circulation and air mass frequencies to assess impacts on ablation and snowfall. A distinct difference in the frequency of different air mass during high SWE versus low SWE years was evident. High SWE years were characterized by substantially greater intrusions of the coldest and driest air mass type (dry polar). Low SWE years, in contrast, had a greater frequency of more moderate air masses (dry moderate and moist moderate). In years with above average SWE, negative departures in November,December,January,February composite 700 hPa field were evident across the continental USA and indicate a greater frequency of troughing across the study area. Low SWE years were characterized by a ridging pattern that reduced the likelihood of precipitation and may have aided in the intrusion of more moderate air masses. Copyright © 2003 Royal Meteorological Society [source] Binary copolymerization with full depropagation: A study of methyl methacrylate/,-methyl styrene copolymerizationJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 17 2005M. J. Leamen Abstract The kinetics of the copolymerization of ,-methyl styrene and methyl methacrylate (MMA) have been revisited for the bulk system. Reactivity ratios and other kinetic parameter estimates based upon a copolymerization model developed by Kruger et al. (Makromol Chemie 1987, 188, 2163,2175) have been determined for a range of temperatures (60,140 °C). An interesting phenomenon has been uncovered, which shows that there is a distinct difference in copolymer composition predicted by the model when compared with experimental data at feed ratios of MMA below a critical value. This deviation also appears to be influenced by the reaction temperature. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 3868,3877, 2005 [source] Views on nurse prescribing: a survey of community mental health nurses in the Republic of IrelandJOURNAL OF PSYCHIATRIC & MENTAL HEALTH NURSING, Issue 1 2009J. WELLS phd rpn A nurse prescribing scheme has recently been implemented within the Republic of Ireland. This paper reports on the views of community mental health nurses on nurse prescribing just prior to the implementation of the scheme. Data were gathered through a 13-item questionnaire administered to 103 members of the Association of Community Mental Health Nurses in Ireland. Results indicated a distinct difference of view between male and female community mental health nurses, with female nurses having greater reservations towards the desirability of nurse prescribing in relation to educational preparation and impact on professional relationships. Overall, only 17% of respondents favoured being supervised in their prescribing practice by their consultant psychiatrist. The paper concludes that there is ambivalence towards prescribing in this important group of nurses which may need to be taken into account if nurse prescribing is to be successfully implemented within the Irish mental health service context. [source] The Deal Structuring Stage of the Venture Capitalist Decision-Making Process: Exploring Confidence and Control,JOURNAL OF SMALL BUSINESS MANAGEMENT, Issue 2 2009G. Tyge Payne This exploratory study examines the deal structuring stage of the venture capitalist decision-making process. Here, the primary issues of concern are investor confidence and potential control of a venture in relation to the level of financing the investor provides and the structure with which the funding is delivered. Confidence comes in support of the entrepreneur, the venture itself, or a combination of the two, prior to capital transfer, but after the initial "invest or not invest" decision has already occurred. Findings support a multicriteria perspective of the pre-investment decision-making process and a distinct difference between entrepreneur confidence and venture confidence in the deal structuring stage. [source] Characterization of ,-tubulin gene distinctively presented in a cytoplasmic male sterile and its maintainer line of non-heading Chinese cabbageJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 2 2009Jingyi Zhang Abstract BACKGROUND: Microtubules are prominent components of the cytoskeleton in every eukaryotic cell. Plant microtubules are essential for a wide variety of cellular functions, including generation of cell polarity, intracellular transport, positioning of organelles, cell wall deposition and cell division. The major component of microtubules is tubulin, an ,,, heterodimer protein with a molecular mass of each subunit of around 50 kDa. Tubulin exists in cells as a mixture of polypeptides differing in their isoelectric points. Some post-translational modifications of tubulins are thought to modulate the functions and localization of microtubules within the cell. RESULTS: The complete sequence of a single-copy ,-tubulin gene Tuba1, belonging to a multiple gene family of non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino), was obtained. The gene was expressed in high levels in young leaves and stamens, and it was also highly expressed during all stages of microsporogenesis in the maintainer. However, there was a distinct difference in ,-tubulin expression between the sterile stage and the normal stages of pollen in a cytoplasmic male sterility line and its maintainer. CONCLUSION:Tuba1 was significantly related to the cell division and elongation of non-heading Chinese cabbage, demonstrating that this gene played an important role in the development of pollen and may be closely related to male sterility. Copyright © 2008 Society of Chemical Industry [source] Morphophysiological dormancy in seeds of three eastern North American Sanicula species (Apiaceae subf.PLANT SPECIES BIOLOGY, Issue 2 2010Saniculoideae): evolutionary implications for dormancy break Abstract Dormancy breaking and germination requirements were determined for seeds of the eastern North American (eNA) species Sanicula canadensis, Sanicula gregaria and Sanicula trifoliata, and the data compared to those available for the European,Asian (EurA) congener Sanicula europaea. Seeds of the three eNA species had underdeveloped embryos that were physiologically dormant, i.e., morphophysiological dormancy (MPD). Warm (25/15°C) followed by cold (5/1°C) stratification was effective in breaking dormancy in 100% of the S. canadensis seeds, but in only 29.3% of S. gregaria seeds and 43.3% of S. trifoliata seeds. Cold stratification alone broke dormancy in 38.7, 12.0 and 0% of S. canadensis, S. gregaria and S. trifoliata seeds, respectively. Thus, some seeds of S. canadensis and of S. gregaria that germinated have non-deep complex MPD, and others have deep complex MPD. All seeds of S. trifoliata that germinated have non-deep complex MPD. Within a phylogenetic context, the kind (level) of MPD may or may not differ between eNA Sanicula sister species because conspecific variation in the kind of MPD exists in seeds of S. canadensis and S. gregaria. Similarly, the kind of MPD in seeds of eNA S. canadensis and S. gregaria may or may not differ with the deep complex MPD in seeds of the EurA S. europaea. However, the non-deep complex MPD in all seeds of eNA S. trifoliata and deep complex MPD in seeds of S. europaea represent a distinct difference in this trait between two of the five clades comprising the genus Sanicula. [source] Lack of evidence of monomer/misfolded superoxide dismutase-1 in sporadic amyotrophic lateral sclerosis,ANNALS OF NEUROLOGY, Issue 1 2009Hsueh-Ning Liu PhD Objective In familial amyotrophic lateral sclerosis (fALS) harboring superoxide dismutase (SOD1) mutations (fALS1), SOD1 toxicity has been linked to its propensity to misfold and aggregate. It has recently been proposed that misfolded SOD1 may be causative of all types of ALS, including sporadic cases (sALS). In the present study, we have used a specific antibody to test for the presence of monomer/misfolded SOD1 in sALS. Methods Sections from lumbar spinal cords of 5 fALS1 cases, 13 sALS cases, and 1 non-SOD1 fALS case were labeled immunocytochemically using SOD1-exposed-dimer-interface (SEDI) antibody, which we have previously validated as being specific for pathological monomer/misfolded forms of SOD1. Results Monomer/misfolded SOD1 was detected with SEDI antibody in all 5 of the fALS1 cases, localizing predominantly to hyaline conglomerate inclusions, a specific pathological feature of fALS1. In contrast, monomer/misfolded SOD1 was not detected in any of the 13 sALS cases or in the non-SOD1 fALS cases. These results were confirmed by immunoprecipitation. Interpretation Although SEDI antibody does not necessarily label all misfolded forms of SOD1, these findings show a distinct difference between fALS1 and sALS, and do not support that monomer/misfolded SOD1 is a common disease entity linking all types of ALS. This is important to our understanding of ALS disease pathogenesis and to considerations of the applicability of using therapeutics that target misfolded SOD1 to non-SOD1-related cases. Ann Neurol 2009;66:75,80 [source] Spatial variability of soil and nutrient characteristics of semi-arid grasslands and shrublands, Jornada Basin, New MexicoECOHYDROLOGY, Issue 1 2008Eva Nora Mueller Abstract Heterogeneity of vegetation and soil properties is characteristic of semi-arid and arid environments. The potential underlying causes of the dynamics that create this spatial variability, with consequent impacts on landscape connectivity and thus ecological and ecohydrological processes, are not clearly understood. An investigation was carried out into the spatial variability of ponded infiltration rate, soil moisture, soil-aggregate stability, vegetation cover, random roughness and nutrient content in the soil (ammonium, nitrate and phosphorus) at grassland and shrubland sites for two spatial scales in the Jornada Basin, in the northern part of the Chihuahua desert. At the plant-interplant scale, statistically significant differences exist between vegetated and non-vegetated sites for soil moisture and infiltration rate within both shrublands and grasslands. The spatial distributions of all other parameters follow a more complex scheme at this scale. At the landscape scale, distinct differences exist for most parameters between the grasslands and the shrubland sites. Geostatistical analysis revealed that the autocorrelation lengths are not simply a function of average shrub sizes, but may be caused by a more complex pattern probably related to the spatial layout of rill and inter-rill areas and other localized transfers of soil resources through the redistribution of water and wind. These results demonstrate the importance of understanding spatial linkages of processes within the landscape in understanding dryland ecosystem dynamics. Copyright © 2007 John Wiley & Sons, Ltd. [source] Sugarcane proteomics: Establishment of a protein extraction method for 2-DE in stalk tissues and initiation of sugarcane proteome reference mapELECTROPHORESIS, Issue 12 2010Ramesh Sundar Amalraj Abstract Sugarcane is an important commercial crop cultivated for its stalks and sugar is a prized commodity essential in human nutrition. Proteomics of sugarcane is in its infancy, especially when dealing with the stalk tissues, where there is no study to date. A systematic proteome analysis of stalk tissue yet remains to be investigated in sugarcane, wherein the stalk tissue is well known for its rigidity, fibrous nature, and the presence of oxidative enzymes, phenolic compounds and extreme levels of carbohydrates, thus making the protein extraction complicated. Here, we evaluated five different protein extraction methods in sugarcane stalk tissues. These methods are as follows: direct extraction using lysis buffer (LB), TCA/acetone precipitation followed by solubilization in LB, LB containing thiourea (LBT), and LBT containing tris, and phenol extraction. Both quantitative and qualitative protein analyses were performed for each method. 2-DE analysis of extracted total proteins revealed distinct differences in protein patterns among the methods, which might be due to their physicochemical limitations. Based on the 2-D gel protein profiles, TCA/acetone precipitation-LBT and phenol extraction methods showed good results. The phenol method showed a shift in pI values of proteins on 2-D gel, which was mostly overcome by the use of 2-D cleanup kit after protein extraction. Among all the methods tested, 2-D cleanup-phenol method was found to be the most suitable for producing high number of good-quality spots and reproducibility. In total, 30 and 12 protein spots commonly present in LB, LBT and phenol methods, and LBT method were selected and subjected to eLD -IT-TOF-MS/MS and nESI-LC-MS/MS analyses, respectively, and a reference map has been established for sugarcane stalk tissue proteome. A total of 36 nonredundant proteins were identified. This is a very first basic study on sugarcane stalk proteome analysis and will promote the unexplored areas of sugarcane proteome research. [source] Prokaryotic diversity and metabolically active microbial populations in sediments from an active mud volcano in the Gulf of MexicoENVIRONMENTAL MICROBIOLOGY, Issue 10 2006Robert J. Martinez Summary In this study, ribosomes and genomic DNA were extracted from three sediment depths (0,2, 6,8 and 10,12 cm) to determine the vertical changes in the microbial community composition and identify metabolically active microbial populations in sediments obtained from an active seafloor mud volcano site in the northern Gulf of Mexico. Domain-specific Bacteria and Archaea 16S polymerase chain reaction primers were used to amplify 16S rDNA gene sequences from extracted DNA. Complementary 16S ribosomal DNA (crDNA) was obtained from rRNA extracted from each sediment depth that had been subjected to reverse transcription polymerase chain reaction amplification. Twelve different 16S clone libraries, representing the three sediment depths, were constructed and a total of 154 rDNA (DNA-derived) and 142 crDNA (RNA-derived) Bacteria clones and 134 rDNA and 146 crDNA Archaea clones obtained. Analyses of the 576 clones revealed distinct differences in the composition and patterns of metabolically active microbial phylotypes relative to sediment depth. For example, ,- Proteobacteria rDNA clones dominated the 0,2 cm clone library whereas ,-Proteobacteria dominated the 0,2 cm crDNA library suggesting , to be among the most active in situ populations detected at 0,2 cm. Some microbial lineages, although detected at a frequency as high as 9% or greater in the total DNA library (i.e. Actinobacteria, ,- Proteobacteria), were markedly absent from the RNA-derived libraries suggesting a lack of in situ activity at any depth in the mud volcano sediments. This study is one of the first to report the composition of the microbial assemblages and physiologically active members of archaeal and bacterial populations extant in a Gulf of Mexico submarine mud volcano. [source] A dual symbiosis shared by two mussel species, Bathymodiolus azoricus and Bathymodiolus puteoserpentis (Bivalvia: Mytilidae), from hydrothermal vents along the northern Mid-Atlantic RidgeENVIRONMENTAL MICROBIOLOGY, Issue 8 2006Sébastien Duperron Summary Bathymodiolus azoricus and Bathymodiolus puteoserpentis are symbiont-bearing mussels that dominate hydrothermal vent sites along the northern Mid-Atlantic Ridge (MAR). Both species live in symbiosis with two physiologically and phylogenetically distinct Gammaproteobacteria: a sulfur-oxidizing chemoautotroph and a methane-oxidizer. A detailed analysis of mussels collected from four MAR vent sites (Menez Gwen, Lucky Strike, Rainbow, and Logatchev) using comparative 16S rRNA sequence analysis and fluorescence in situ hybridization (FISH) showed that the two mussel species share highly similar to identical symbiont phylotypes. FISH observations of symbiont distribution and relative abundances showed no obvious differences between the two host species. In contrast, distinct differences in relative symbiont abundances were observed between mussels from different sites, indicating that vent chemistry may influence the relative abundance of thiotrophs and methanotrophs in these dual symbioses. [source] Trace metal distribution in soluble organic matter from municipal solid waste compost determined by size-exclusion chromatographyENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 9 2002Arno Kaschl Abstract Municipal solid waste (MSW) composts carry high amounts of trace metals and organic complexing agents that may influence metal bioavailability and mobility after application to soils. In order to assess the degree of organic complexation of trace metals in the solution phase of MSW compost and the relevance of organic ligand type, size exclusion chromatography (SEC) was applied to compost-extracted organic ligands. Adjustment of the elution conditions minimized the interaction with the gel matrix for compost humic substances and dissolved organic matter (DOM) fractions. The SEC was then used to separate the aqueous compost extract into samples with distinct differences in chemical constituents. The highest quantities of Cu, Zn, Ni, Mn, and Cd were found to coelute with the main peak of the SEC elution curve, which, as observed by Fourier-transformed infrared (FTIR) spectroscopy, also had the highest density of carboxyl groups. The ratio of aromatic to aliphatic structures was higher for eluates with low retention times, and cations such as Al, Cr, and Fe were preferably associated with these larger organic molecules. All trace metals in the compost solution phase were bound mostly to DOM rather than forming inorganic complexes. [source] Expression of the human Cathepsin L inhibitor hurpin in mice: skin alterations and increased carcinogenesisEXPERIMENTAL DERMATOLOGY, Issue 9 2007Markus Walz Abstract:, The serine protease inhibitor (serpin) hurpin (serpin B13) is a cross class-specific inhibitor of the cysteine protease Cathepsin (Cat) L. Cat L is involved in lysosomal protein degradation, hair follicle morphogenesis, epidermal differentiation and epitope generation of antigens. Hurpin is a 44 kDa protein which is expressed predominantly in epidermal cells. In psoriatic skin samples, hurpin was strongly overexpressed when compared with normal skin. Keratinocytes overexpressing hurpin showed increased resistance towards UVB-induced apoptosis. To further analyse the functional importance of this inhibitor, we have generated transgenic mice with deregulated Cat L activity by expressing human hurpin in addition to the endogenous mouse inhibitor. The three independent transgenic lines generated were characterized by identical effects excluding insertional phenotypes. Macroscopically, mice expressing human hurpin are characterized by abnormal abdominal fur. The number of apoptotic cells and caspase-3 positive cells was reduced after UV-irradiation in transgenic animals compared with wild-type mice. Interestingly, after chemical carcinogenesis, transgenic mice showed an increased susceptibility to develop skin cancer. Array analysis of gene expression revealed distinct differences between wild-type and hurpin-transgenic mice. Among others, differentially expressed genes are related to antigen presentation and angiogenesis. These results suggest an important role of Cat L regulation by hurpin which might be of clinical relevance in human skin diseases. [source] Identification of Atlantic bluefin tuna (Thunnus thynnus) stocks from putative nurseries using otolith chemistryFISHERIES OCEANOGRAPHY, Issue 2 2003Jay R. Rooker Abstract Chemical signatures in the otoliths of teleost fishes represent natural tags that may reflect differences in the chemical and physical characteristics of an individuals' environment. Otolith chemistry of Atlantic bluefin tuna (Thunnus thynnus) was quantified to assess the feasibility of using these natural tags to discriminate juveniles (age 0 and age 1) from putative nurseries. A suite of six elements (Li, Mg, Ca, Mn, Sr and Ba) was measured in whole otoliths using solution-based inductively coupled plasma mass spectrometry. Otolith chemistry of age-1 T. thynnus collected from the two primary nurseries in the Mediterranean Sea and western Atlantic Ocean differed significantly, with a cross-validated classification accuracy of 85%. Spatial and temporal variation in otolith chemistry was evaluated for age-0 T. thynnus collected from three nurseries within the Mediterranean Sea: Alboran Sea (Spain), Ligurian Sea (northern Italy), and Tyrrhenian Sea (southern Italy). Distinct differences in otolith chemistry were detected among Mediterranean nurseries and classification accuracies ranged from 62 to 80%. Interannual trends in otolith chemistry were observed between year classes of age-0 T. thynnus in the Alboran Sea; however, no differences were detected between year classes in the Tyrrhenian Sea. Age-0 and age-1 T. thynnus collected from the same region (Ligurian Sea) were also compared and distinct differences in otolith chemistry were observed, indicating ontogenetic shifts in habitat or elemental discrimination. Findings suggest that otolith chemistry of juvenile T. thynnus from different nurseries are distinct and chemical signatures show some degree of temporal persistence, indicating the technique has considerable potential for use in future assessments of population connectivity and stock structure of T. thynnus. [source] Papillary and muscle invasive bladder tumors with distinct genomic stability profiles have different DNA repair fidelity and KU DNA-binding activitiesGENES, CHROMOSOMES AND CANCER, Issue 4 2009Johanne Bentley Low-grade noninvasive papillary bladder tumors are genetically stable whereas muscle invasive bladder tumors display high levels of chromosomal aberrations. As cells deficient for nonhomologous end-joining (NHEJ) pathway components display increased genomic instability, we sought to determine the NHEJ repair characteristics of bladder tumors and correlate this with tumor stage and grade. A panel of 13 human bladder tumors of defined stage and grade were investigated for chromosomal aberrations by comparative genomic hybridization and for NHEJ repair fidelity and function. Repair assays were conducted with extracts made directly from bladder tumor specimens to avoid culture-induced phenotypic alterations and selection bias as only a minority of bladder tumors grow in culture. Four noninvasive bladder tumors (pTaG2), which were genetically stable, repaired a partially incompatible double-strand break (DSB) by NHEJ-dependent annealing of termini and fill-in of overhangs with minimal loss of nucleotides. In contrast, four muscle invasive bladder cancers (pT2-3G3), which displayed gross chromosomal rearrangements, repaired DSBs in an error-prone manner involving extensive resection and microhomology association. Four minimally invasive bladder cancers (pT1G3) had characteristics of both repair types. Error-prone repair in bladder tumors correlated with reduced KU DNA-binding and loss of TP53 function. In conclusion, there were distinct differences in DSB repair between noninvasive papillary tumors and higher stage/grade invasive cancers. End-joining fidelity correlated with stage and was increasingly error-prone as tumors became more invasive and KU binding activity reduced; these changes may underlie the different genomic profiles of these tumors. © 2008 Wiley-Liss, Inc. [source] Detection of elafin as a candidate biomarker for ulcerative colitis by whole-genome microarray screeningINFLAMMATORY BOWEL DISEASES, Issue 9 2006Carl-Fredrik Flach PhD Abstract The cause of ulcerative colitis (UC) is largely unknown. Microarray studies are an efficient way of investigating the various genes involved. Here, we have used whole-genome microarrays to clarify the clinical picture and to identify new biomarkers for improved diagnosis. Rectal biopsies were taken from five UC patients and five matched controls, and RNA transcripts were prepared. After labeling, each sample was individually applied to the microarray chips. All transcripts that were more than 10-fold up-regulated in all five patients were analyzed further in seven additional patients and seven controls using quantitative polymerase chain reaction. Of 47,000 transcripts examined, 4 were highly up-regulated in all patients: those encoding elafin, a secreted protease inhibitor, the ion and amino acid transporter B0,+ (SLC6A14), and the metabolic enzyme aldolase B, as well as a recently identified transcript named similar to numb-interacting homolog. The up-regulation of these transcripts appears to follow the progression of the disease because elevated expression was detected in the proximal part of the colon in patients with total colitis but not in patients with left-sided colitis. Immunohistologic examination showed very distinct differences in the expression of elafin. Extensive expression was detected in enterocytes and goblet cells of the affected mucosa, whereas there was no detectable expression in unaffected mucosa and in healthy controls. The results implicate four transcripts and proteins of special interest as possible targets for pharmacologic interference and as biomarkers in UC. Of these, elafin may be of special interest because it is a secreted protein that may be measured in body fluids. [source] Gene expression associated with changes in cold tolerance levels of the Antarctic springtail, Cryptopygus antarcticusINSECT MOLECULAR BIOLOGY, Issue 1 2010G. Burns Abstract The ability of the Antarctic microarthropod Cryptopygus antarcticus (Collembola, Isotomidae) to survive low temperatures has been well studied at the physiological level, with recent investigations indicating the importance of the moulting process in conferring this ability. This study investigated gene expression in groups of C. antarcticus that have distinct differences in their ability to survive low temperatures. A microarray containing c. 5400 C. antarcticus expressed sequence tags was used to investigate gene expression differences between groups of animals with different supercooling points (SCP), and to low temperatures close to their SCP. By demonstrating the involvement of moult-related genes in the differential survival of two groups of C. antarcticus with distinct SCP profiles, the results of this investigation add support to the suggestion that moulting plays a role in conferring cold tolerance in C. antarcticus. [source] Distinct CpG island methylation profiles and BRAF mutation status in serrated and adenomatous colorectal polypsINTERNATIONAL JOURNAL OF CANCER, Issue 11 2008Yong Ho Kim Abstract A subset of colorectal cancers with CpG island methylator phenotype-high (CIMP-H) is frequently associated with MSI and BRAF V600E mutation. Since limited data are available on different histological types of colorectal polyps, we compared the pattern and the frequency of promoter methylation, CIMP-H, MSI, KRAS and BRAF V600E mutations and the relationship among these molecular parameters and the clinicopathologic characteristics in 110 serrated polyps (48 hyperplastic polyps, 32 sessile serrated adenomas and 30 serrated adenomas) and 32 tubular adenomas using 7 commonly used tumor-associated gene loci. No significant difference in the frequency of overall methylation frequency (86% vs. 100%) and CIMP-H (39% vs. 28%) between serrated polyps and tubular adenomas was observed, but proximally located serrated polyps showed more frequent methylation at 5 of 7 loci examined, and were more likely to be CIMP-H (62% vs. 22%). MGMT methylation was more common in tubular adenomas while MLH1 and HIC1 were more frequently methylated in serrated polyps. BRAF mutation was frequently present in all types of serrated polyps (80%), but was absent in tubular adenomas and was not associated with CIMP or MSI status. These results show comparable frequencies of promoter methylation of tumor-associated genes and CIMP-H, but distinct differences in gene-specific or colonic site-specific methylation profiles occur in serrated polyps and tubular adenomas. BRAF mutation occurs independently of CIMP and MSI in all types of serrated polyps and may serve as a marker of serrated pathway of colorectal carcinogenesis. © 2008 Wiley-Liss, Inc. [source] Frequent amplification and overexpression of CCND1 in male breast cancerINTERNATIONAL JOURNAL OF CANCER, Issue 6 2004Maarit Bärlund Abstract Genetic events underlying the pathogenesis of breast cancer have been studied extensively and several clinically significant markers have been identified. For example, amplification and overexpression of the ERBB2 oncogene is associated with poor prognosis in breast cancer and ERBB2 serves as a target for antibody-based therapy. Current knowledge on the pathogenesis of male breast cancer (MBC) is limited. The purpose of our study was to investigate the potential relevance of a series of genes known to be amplified in female breast cancer (FBC) in a the development and pathogenesis of MBC. To this end, we applied fluorescence in situ hybridization and immunohistochemistry to the analysis of 128 breast tumors from males. Amplification of ERBB2, MYC, PPM1D and ZNF217 was detected rarely (1,2% of tumors) indicating a considerably lower amplification frequency than in FBC. CCND1 amplification was observed in 12% of cases, being in good concordance with findings from FBC. In addition, CCND1 overexpression was detected in 63% of tumors and was associated with ER positivity (p < 0.0001). Our results indicate distinct differences in the genetic basis of MBC and FBC and suggest that marked differences exist in the pathogenesis of these diseases. The lack of ERBB2 involvement was especially unexpected and implies that ERBB2 -targeted therapies are unlikely to be beneficial in MBC. Furthermore, the high frequency of hormone receptor positivity and the association between ER positivity and CCND1 overexpression supports the notion that hormonal regulation is likely to be essential for the development of MBC. © 2004 Wiley-Liss, Inc. [source] DFT study of polymorphism of the DNA double helix at the level of dinucleoside monophosphatesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2010Valeri I. Poltev Abstract We apply DFT calculations to deoxydinucleoside monophosphates (dDMPs) which represent minimal fragments of the DNA chain to study the molecular basis of stability of the DNA duplex, the origin of its polymorphism and conformational heterogeneity. In this work, we continue our previous studies of dDMPs where we detected internal energy minima corresponding to the "classical" B conformation (BI-form), which is the dominant form in the crystals of oligonucleotide duplexes. We obtained BI local energy minima for all existing base sequences of dDMPs. In the present study, we extend our analysis to other families of DNA conformations, successfully identifying A, BI, and BII energy minima for all dDMP sequences. These conformations demonstrate distinct differences in sugar ring puckering, but similar sequence-dependent base arrangements. Internal energies of BI and BII conformers are close to each other for nearly all the base sequences. The dGpdG, dTpdG, and dCpdA dDMPs slightly favor the BII conformation, which agrees with these sequences being more frequently experimentally encountered in the BII form. We have found BII-like structures of dDMPs for the base sequences both existing in crystals in BII conformation and those not yet encountered in crystals till now. On the other hand, we failed to obtain dDMP energy minima corresponding to the Z family of DNA conformations, thus giving us the ground to conclude that these conformations are stabilized in both crystals and solutions by external factors, presumably by interactions with various components of the media. Overall the accumulated computational data demonstrate that the A, BI, and BII families of DNA conformations originate from the corresponding local energy minimum conformations of dDMPs, thus determining structural stability of a single DNA strand during the processes of unwinding and rewinding of DNA. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2548,2559, 2010 [source] | |||||||||||||||||||||||||||||||||||||||||||