Showing papers by "Leibniz Association published in 2003"

Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.).

Abstract: A software tool was developed for the identification of simple sequence repeats (SSRs) in a barley (Hordeum vulgare L.) EST (expressed sequence tag) database comprising 24,595 sequences. In total, 1,856 SSR-containing sequences were identified. Trimeric SSR repeat motifs appeared to be the most abundant type. A subset of 311 primer pairs flanking SSR loci have been used for screening polymorphisms among six barley cultivars, being parents of three mapping populations. As a result, 76 EST-derived SSR-markers were integrated into a barley genetic consensus map. A correlation between polymorphism and the number of repeats was observed for SSRs built of dimeric up to tetrameric units. 3′-ESTs yielded a higher portion of polymorphic SSRs (64%) than 5′-ESTs did. The estimated PIC (polymorphic information content) value was 0.45 ± 0.03. Approximately 80% of the SSR-markers amplified DNA fragments in Hordeum bulbosum, followed by rye, wheat (both about 60%) and rice (40%). A subset of 38 EST-derived SSR-markers comprising 114 alleles were used to investigate genetic diversity among 54 barley cultivars. In accordance with a previous, RFLP-based, study, spring and winter cultivars, as well as two- and six-rowed barleys, formed separate clades upon PCoA analysis. The results show that: (1) with the software tool developed, EST databases can be efficiently exploited for the development of cDNA-SSRs, (2) EST-derived SSRs are significantly less polymorphic than those derived from genomic regions, (3) a considerable portion of the developed SSRs can be transferred to related species, and (4) compared to RFLP-markers, cDNA-SSRs yield similar patterns of genetic diversity.

Map-based isolation of the leaf rust disease resistance gene Lr10 from the hexaploid wheat (Triticum aestivum L.) genome

Abstract: More than 50 leaf rust resistance (Lr) genes against the fungal pathogen Puccinia triticina have been identified in the wheat gene pool, and a large number of them have been extensively used in breeding. Of the 50 Lr genes, all are known only from their phenotype and/or map position except for Lr21, which was cloned recently. For many years, the problems of molecular work in the large (1.6 × 1010 bp), highly repetitive (80%), and hexaploid bread wheat (Triticum aestivum L.) genome have hampered map-based cloning. Here, we report the isolation of the Lr gene Lr10 from hexaploid wheat by using a combination of subgenome map-based cloning and haplotype studies in the genus Triticum. Lr10 is a single-copy gene on chromosome 1AS. It encodes a CC-NBS-LRR type of protein with an N-terminal domain, which is under diversifying selection. When overexpressed in transgenic wheat plants, Lr10 confers enhanced resistance to leaf rust. Lr10 has similarities to RPM1 in Arabidopsis thaliana and to resistance gene analogs in rice and barley, but is not closely related to other wheat Lr genes based on Southern analysis. We conclude that map-based cloning of genes of agronomic importance in hexaploid wheat is now feasible, opening perspectives for molecular bread wheat improvement trough transgenic strategies and diagnostic allele detection.

Influence of temperature on thermal conductivity, thermal capacity and thermal diffusivity for different types of rock

Abstract: Thermal modeling down to great depth, e.g. down to the Mohorovicic discontinuity, requires representative values of thermal conductivity and thermal capacity at an appropriate depth. Often there is a lack of data, especially concerning temperature and pressure dependence of thermal conductivity and thermal capacity, due to missing or questionable data from boreholes. Studies of the temperature and pressure dependence of thermal conductivity and thermal capacity showed that temperature is dominating. Thus measurements on a set of magmatic, metamorphic and sedimentary rocks sampled from different depth levels of the Eastern Alpine crust were used to obtain an estimate of the temperature dependence of both properties––at least for the area of investigation––and to give a review of the temperature dependence of thermal conductivity ( λ ), thermal capacity ( ρ × c p ) and thermal diffusivity ( κ ) for different types of rock. The temperature dependence of thermal conductivity for crystalline (magmatitic and metamorphic) rocks is different to that of sedimentary rocks. Using the approach that the thermal resistivity (1/ λ ) is a linear function of temperature whose slope increases with λ (0), the conductivity at a temperature of 0 °C, two general equations were determined. The equation for crystalline rocks was verified in the temperature range of 0–500 °C and the equation for sedimentary rocks was tested in the temperature range from 0 to 300 °C. A general equation for the temperature dependence of λ for Eastern Alpine rocks can thus be formulated: λ(T)= λ(0) 0.99+T(a−b/λ(0)) with empirical constants and corresponding uncertainties a =0.0030±0.0015 and b =0.0042±0.0006 for crystalline rocks. The constants for corresponding sedimentary rocks are a =0.0034±0.0006 and b =0.0039±0.0014. λ is given in W m −1 K −1 , T in °C. At ambient conditions thermal diffusivity ( κ ) and thermal conductivity ( λ ) for Eastern Alpine crystalline rocks show the relationship: κ=0.45×λ.

The nature and identification of quantitative trait loci: a community's view.

Abstract: This white paper by eighty members of the Complex Trait Consortium presents a community's view on the approaches and statistical analyses that are needed for the identification of genetic loci that determine quantitative traits. Quantitative trait loci (QTLs) can be identified in several ways, but is there a definitive test of whether a candidate locus actually corresponds to a specific QTL?

Mutations in factor H reduce binding affinity to C3b and heparin and surface attachment to endothelial cells in hemolytic uremic syndrome

Abstract: Hemolytic uremic syndrome (HUS) is a disease characterized by microangiopathic hemolytic anemia, thrombocytopenia, and acute renal failure Recent studies have identified a factor H–associated form of HUS, caused by gene mutations that cluster in the C-terminal region of the complement regulator factor H Here we report how three mutations (E1172Stop, R1210C, and R1215G; each of the latter two identified in three independent cases from different, unrelated families) affect protein function All three mutations cause reduced binding to the central complement component C3b/C3d to heparin, as well as to endothelial cells These defective features of the mutant factor H proteins explain progression of endothelial cell and microvascular damage in factor H–associated genetic HUS and indicate a protective role of factor H for tissue integrity during thrombus formation

Review of mesospheric temperature trends

Abstract: In recent times it has become increasingly clear that releases of trace gases from human activity have a potential for causing change in the upper atmosphere. However, our knowledge of systematic changes and trends in the temperature of the mesosphere and lower thermosphere is relatively limited compared to the Earths lower atmosphere, and not much effort has been made to synthesize these results so far. In this article, a comprehensive review of long-term trends in the temperature of the region from 50 to 100 km is made on the basis of the available up-to-date understanding of measurements and model calculations. An objective evaluation of the available data sets is attempted, and important uncertainly factors are discussed. Some natural variability factors, which are likely to play a role in modulating temperature trends, are also briefly touched upon. There are a growing number of experimental results centered on, or consistent with, zero temperature trend in the mesopause region (80–100 km). The most reliable data sets show no significant trend but an uncertainty of at least 2 K/decade. On the other hand, a majority of studies indicate negative trends in the lower and middle mesosphere with an amplitude of a few degrees (2–3 K) per decade. In tropical latitudes the cooling trend increases in the upper mesosphere. The most recent general circulation models indicate increased cooling closer to both poles in the middle mesosphere and a decrease in cooling toward the summer pole in the upper mesosphere. Quantitatively, the simulated cooling trend in the middle mesosphere produced only by CO 2 increase is usually below the observed level. However, including other greenhouse gases and taking into account a “thermal shrinking” of the upper atmosphere result in a cooling of a few degrees per decade. This is close to the lower limit of the observed nonzero trends. In the mesopause region, recent model simulations produce trends, usually below 1 K/decade, that appear to be consistent with most observations in this region

Navigation impacts on freshwater fish assemblages: the ecological relevance of swimming performance

Abstract: Waterways provide many ecological and socialservices, such as water supply, navigation,freshwater reservoirs for aquatic organisms,recreation, and fisheries. However, in heavilydeveloped waterways, the diversity andproductivity of fish assemblages typicallybecome reduced, mainly due to migrationbarriers, pollution, habitat loss, and biotopesimplification. Additionally, navigation maydirectly or indirectly reduce fish assemblages,amplifying the effects of habitat destruction.This study summarizes navigation impacts toimprove the evaluation of direct navigationeffects on fish assemblages. Literature onhydraulic forces created by moving tows wasreviewed to compare the pressures induced byshipping with the biological capabilities offish, especially with their swimming speeds.Available studies of swimming performance offreshwater fishes were compiled to developgeneral models of length-specific burst, aswell as critical swimming speeds. Modelsregressing total length on burst and criticalswimming speeds were highly significant.Linking applied hydrology and hydraulicengineering with fish ecology and physiology,absolute speed was concluded to be the bestpredictor for thresholds and limitations ofhabitat use by fish. A navigation-inducedhabitat bottleneck hypothesis (NBH) wasinferred from the threshold flow velocity,determining habitat availability for fish.According to the NBH presented here, swimmingperformance of juvenile freshwater fish is themajor bottleneck for fish recruitment inwaterways, as a result of their inability towithstand bank-directed navigation-inducedphysical forces. In essence, under commonnavigation conditions, with respect to inlandwaterway morphology, channel cross section,vessel speeds, and dimensions of commercialvessels, the navigation-induced return currentsalong the shore are usually around 0.8 ms−1 (0.7–1.0 m s−1) accompanied by a0.1–0.3 m drawdown. Under such conditions, theproposed threshold for small fish survival wasestimated to be 147 mm total length at criticalswimming performance (>20 s – 60 min withoutfatigue) and 47 mm at burst performance (<20s). These theoretical findings were supportedby empirical studies of fish recruitment inwaterways. The strong dependence of fishrecruitment on hydraulic forces opens uppossibilities of formulating suitable criteriafor safe ship operation (speed and distance tobank), as well as for effective fairwaymanagement (construction and maintenance) andsustainable fish conservation (species andproduction). A more ecologically orientatedhydraulic engineering will not constraincommercial navigation and their socioeconomicbenefits, but it will substantially enhancefish recruitment in waterways and theirecological sustainability, for the overallbenefit of fish, fisheries, and society.

Allene oxide cyclase dependence of the wound response and vascular bundle-specific generation of jasmonates in tomato - amplification in wound signalling.

Abstract: The allene oxide cyclase (AOC)-catalyzed step in jasmonate (JA) biosynthesis is important in the wound response of tomato. As shown by treatments with systemin and its inactive analog, and by analysis of 35S::prosysteminsense and 35S::prosysteminantisense plants, the AOC seems to be activated by systemin (and JA) leading to elevated formation of JA. Data are presented on the local wound response following activation of AOC and generation of JA, both in vascular bundles. The tissue-specific occurrence of AOC protein and generation of JA is kept upon wounding or other stresses, but is compromised in 35S::AOCsense plants, whereas 35S::AOCantisense plants exhibited residual AOC expression, a less than 10% rise in JA, and no detectable expression of wound response genes. The (i). activation of systemin-dependent AOC and JA biosynthesis occurring only upon substrate generation, (ii). the tissue-specific occurrence of AOC in vascular bundles, where the prosystemin gene is expressed, and (iii). the tissue-specific generation of JA suggest an amplification in the wound response of tomato leaves allowing local and rapid defense responses.

Methylation of histone H3 in euchromatin of plant chromosomes depends on basic nuclear DNA content.

Abstract: Strong methylation of lysine 4 (K4) and low methylation of lysine 9 (K9) have been proposed as modifications of histone H3, typical for transcriptionally active euchromatin and the opposite for inactive heterochromatin. We have analysed the correlation between the global distribution of histone H3, methylated at either lysine 4 or lysine 9, and of microscopically detectable euchromatic or heterochromatic regions in relation to genome size for 24 plant species. Two different distribution patterns of methylated (K9)H3 (Met(K9)H3) were found that depend on genome size. For most species with small genomes (1C <500 Mbp), including Arabidopsis thaliana, strong methylation of (K9)H3 was restricted to constitutive heterochromatin. Species with larger genomes showed a uniform distribution of Met(K9)H3. Contrary to this and regardless of the genome size, methylated (K4)H3 (Met(K4)H3) was found to be enriched within the euchromatin of all species. Transcriptionally less active B chromosomes showed the same patterns as basic A chromosomes. We thus propose that large genomes with high amounts of dispersed repetitive sequences (mainly retroelements) have to silence these sequences and therefore display epigenetic modifications such as methylation of DNA and (K9)H3 also within euchromatic regions.

Molecular Interactions between the Specialist Herbivore Manduca sexta (Lepidoptera, Sphingidae) and Its Natural Host Nicotiana attenuata: V. Microarray Analysis and Further Characterization of Large-Scale Changes in Herbivore-Induced mRNAs

Abstract: We extend our analysis of the transcriptional reorganization that occurs when the native tobacco, Nicotiana attenuata, is attacked by Manduca sexta larvae by cloning 115 transcripts by mRNA differential display reverse transcription-polymerase chain reaction and subtractive hybridization using magnetic beads (SHMB) from the M. sexta-responsive transcriptome. These transcripts were spotted as cDNA with eight others, previously confirmed to be differentially regulated by northern analysis on glass slide microarrays, and hybridized with Cy3- and Cy5-labeled probes derived from plants after 2, 6, 12, and 24 h of continuous attack. Microarray analysis proved to be a powerful means of verifying differential expression; 73 of the cloned genes (63%) were differentially regulated (in equal proportions from differential display reverse transcription-polymerase chain reaction and SHMB procedures), and of these, 24 (32%) had similarity to known genes or putative proteins (more from SHMB). The analysis provided insights into the signaling and transcriptional basis of direct and indirect defenses used against herbivores, suggesting simultaneous activation of salicylic acid-, ethylene-, cytokinin-, WRKY-, MYB-, and oxylipin-signaling pathways and implicating terpenoid-, pathogen-, and cell wall-related transcripts in defense responses. These defense responses require resources that could be made available by decreases in four photosynthetic-related transcripts, increases in transcripts associated with protein and nucleotide turnover, and increases in transcripts associated with carbohydrate metabolism. This putative up-regulation of defense-associated and down-regulation of growth-associated transcripts occur against a backdrop of altered transcripts for RNA-binding proteins, putative ATP/ADP translocators, chaperonins, histones, and water channel proteins, responses consistent with a major metabolic reconfiguration that underscores the complexity of response to herbivore attack.

Comparing Typological Structures Across Cultures By Multigroup Latent Class Analysis A Primer

Abstract: The advantages of latent class analysis for cross-cultural research in psychology are discussed. The basic principles of multigroup latent class analysis are described and illustrated by an empirical study comparing satisfaction-with-life-domain profiles across two nations (China, United States). In particular, it is shown how various assumptions of measurement invariance across cultures can be tested statistically in the latent class framework.

Non-self recognition, transcriptional reprogramming, and secondary metabolite accumulation during plant/pathogen interactions

Abstract: Disease resistance of plants involves two distinct forms of chemical communication with the pathogen: recognition and defense. Both are essential components of a highly complex, multifaceted defense response, which begins with non-self recognition through the perception of pathogen-derived signal molecules and results in the production, inter alia, of antibiotically active compounds (phytoalexins) and cell wall-reinforcing material around the infection site. To elucidate the molecular details and the genomic basis of the underlying chains of events, we used two different experimental systems: suspension-cultured cells of Petroselinum crispum (parsley) and wild-type as well as mutant plants of Arabidopsis thaliana. Particular emphasis was placed on the structural and functional identification of signal and defense molecules, and on the mechanisms of signal perception, intracellular signal transduction and transcriptional reprogramming, including the structural and functional characterization of the responsible cis-acting gene promoter elements and transacting regulatory proteins. Comparing P. crispum and A. thaliana allows us to distinguish species-specific defense mechanisms from more universal responses, and furthermore provides general insights into the nature of the interactions. Despite the complexity of the pathogen defense response, it is experimentally tractable, and knowledge gained so far has opened up a new realm of gene technology-assisted strategies for resistance breeding of crop plants.

Members of a Readily Enriched β-Proteobacterial Clade Are Common in Surface Waters of a Humic Lake

Abstract: Humic lakes are systems often characterized by irregular high input of dissolved organic carbon (DOC) from the catchment. We hypothesized that specific bacterial groups which rapidly respond to changes in DOC availability might form large populations in such habitats. Seasonal changes of microbial community composition were studied in two compartments of an artificially divided bog lake with contrasting DOC inputs. These changes were compared to community shifts induced during short-term enrichment experiments. Inocula from the two compartments were diluted 1:10 into water from the more DOC-rich compartment, and inorganic nutrients were added to avoid microbial N and P limitation. The dilutions were incubated for a period of 2 weeks. The microbial assemblages were analyzed by cloning and sequencing of 16S rRNA genes and by fluorescence in situ hybridization with specific oligonucleotide probes. β-Proteobacteria from a cosmopolitan freshwater lineage related to Polynucleobacter necessarius (beta II) were rapidly enriched in all treatments. In contrast, members of the class Actinobacteria did not respond to the enhanced availability of DOC by an immediate increase in growth rate, and their relative abundances declined during the incubations. In lake water members of the beta II clade seasonally constituted up to 50% of all microbes in the water column. Bacteria from this lineage annually formed a significantly higher fraction of the microbial community in the lake compartment with a higher allochthonous influx than in the other compartment. Actinobacteria represented a second numerically important bacterioplankton group, but without clear differences between the compartments. We suggest that the pelagic microbial community of the studied system harbors two major components with fundamentally different growth strategies.

Assessing 1D atmospheric solar radiative transfer models: Interpretation and handling of unresolved clouds

Abstract: The primary purpose of this study is to assess the performance of 1D solar radiative transfer codes that are used currently both for research and in weather and climate models. Emphasis is on interpretation and handling of unresolved clouds. Answers are sought to the following questions: (i) How well do 1D solar codes interpret and handle columns of information pertaining to partly cloudy atmospheres? (ii) Regardless of the adequacy of their assumptions about unresolved clouds, do 1D solar codes perform as intended? One clear-sky and two plane-parallel, homogeneous (PPH) overcast cloud cases serve to elucidate 1D model differences due to varying treatments of gaseous transmittances, cloud optical properties, and basic radiative transfer. The remaining four cases involve 3D distributions of cloud water and water vapor as simulated by cloud-resolving models. Results for 25 1D codes, which included two line-by-line (LBL) models (clear and overcast only) and four 3D Monte Carlo (MC) photon transport ...

Cascading predation effects of Daphnia and copepods on microbial food web components

Abstract: 1. We performed a mesocosm experiment to investigate the structuring and cascading effects of two predominant crustacean mesozooplankton groups on microbial food web components. The natural summer plankton community of a mesotrophic lake was exposed to density gradients of Daphnia and copepods. Regression analysis was used to reveal top-down impacts of mesozooplankton on protists and bacteria after days 9 and 15. 2. Selective grazing by copepods caused a clear trophic cascade via ciliates to nanoplankton. Medium-sized (20-40 mum) ciliates (mainly Oligotrichida) were particularly negatively affected by copepods whereas nanociliates (mainly Prostomatida) became more abundant. Phototrophic and heterotrophic nanoflagellates increased significantly with increasing copepod biomass, which we interpret as an indirect response to reduced grazing pressure from the medium-sized ciliates. 3. In Daphnia-treatments, ciliates of all size classes as well as nanoflagellates were reduced directly but the overall predation effect became most strongly visible after 15 days at higher Daphnia biomass. 4. The response of bacterioplankton involved only modest changes in bacterial biomass and cell-size distribution along the zooplankton gradients. Increasing zooplankton biomass resulted either in a reduction (with Daphnia) or in an increase (with copepods) of bacterial biovolume, activity and production. Patterns of bacterial diversity, as measured by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), showed no distinct grouping after 9 days, whereas a clear treatment-coupled similarity clustering occurred after 15 days. 5. The experiment demonstrated that zooplankton-mediated predatory interactions cascade down to the bacterial level, but also revealed that changes occurred rather slowly in this summer plankton community and were most pronounced with respect to bacterial activity and composition.

A Nonlinear Theory for El Niño Bursting

Abstract: A new mechanism is proposed that explains two key features of the observed El Nino–Southern Oscillation (ENSO) phenomenon—its irregularity and decadal amplitude changes. Using a low-order ENSO model, the authors show that the nonlinearities in the tropical heat budget can lead to bursting behavior characterized by decadal occurrences of strong El Nino events. La Nina events are not affected, a feature that is also seen in ENSO observations. One key result of this analysis is that decadal variability in the Tropics can be generated without invoking extratropical processes or stochastic forcing. The El Nino bursting behavior simulated by the low-order ENSO model can be understood in terms of the concept of homoclinic and heteroclinic connections. It is shown that this new model for ENSO amplitude modulations and irregularity, although difficult to prove, might explain some features of ENSO dynamics seen in more complex climate models and the observations.

Reproduction biology of pikeperch (Sander lucioperca (L.)) – a review

Abstract: – The present review focuses on the reproduction biology of pikeperch (Sander lucioperca (L.)). Aspects like maturity, fecundity, spawning migrations, spawning habitats, onset of spawning, and development time of eggs were reviewed. The onset of maturity is reached at younger age in southern than northern populations due to higher growth rate in the south. Males mature at smaller size and are on average younger than females. Absolute fecundity is closely related to the length and weight, but no clear relationship could be found between relative fecundity and length. Statistically significant relationships were found between the onset of spawning and latitude, and between the duration of the development time of eggs and stable water temperature. Near the southern limits of distribution, the onset of spawning is in February while near the northern limits it is in June. The interannual variability in fecundity and in the onset of maturity and further the factors affecting them have not been studied much. Furthermore, it is not known whether these variations could affect the population dynamics of pikeperch. Little is also known about the actual spawning behaviour of pikeperch in natural habitats. This is probably due to the typical spawning habitats located at 1–3 m depth in waters with high turbidity and low visibility. Even though the homing behaviour to the same spawning areas is well developed in adults, it is not known whether the adults were actually born in the same area.