Showing papers by "Leibniz Association published in 2007"

A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1

Abstract: We performed a genome-wide association study of 19,779 nonsynonymous SNPs in 735 individuals with Crohn disease and 368 controls. A total of 7,159 of these SNPs were informative. We followed up on all 72 SNPs with P 0.4), these data suggest that the underlying biological process may be specific to Crohn disease.

Ecology: managing evolving fish stocks.

Abstract: Evolutionary impact assessment is a framework for quantifying the effects of harvest-induced evolution on the utility generated by fish stocks

Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene

Abstract: Increased seed production has been a common goal during the domestication of cereal crops, and early cultivators of barley (Hordeum vulgare ssp. vulgare) selected a phenotype with a six-rowed spike that stably produced three times the usual grain number. This improved yield established barley as a founder crop for the Near Eastern Neolithic civilization. The barley spike has one central and two lateral spikelets at each rachis node. The wild-type progenitor (H. vulgare ssp. spontaneum) has a two-rowed phenotype, with additional, strictly rudimentary, lateral rows; this natural adaptation is advantageous for seed dispersal after shattering. Until recently, the origin of the six-rowed phenotype remained unknown. In the present study, we isolated vrs1 (six-rowed spike 1), the gene responsible for the six-rowed spike in barley, by means of positional cloning. The wild-type Vrs1 allele (for two-rowed barley) encodes a transcription factor that includes a homeodomain with a closely linked leucine zipper motif. Expression of Vrs1 was strictly localized in the lateral-spikelet primordia of immature spikes, suggesting that the VRS1 protein suppresses development of the lateral rows. Loss of function of Vrs1 resulted in complete conversion of the rudimentary lateral spikelets in two-rowed barley into fully developed fertile spikelets in the six-rowed phenotype. Phylogenetic analysis demonstrated that the six-rowed phenotype originated repeatedly, at different times and in different regions, through independent mutations of Vrs1.

Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans

Abstract: In the postgenomic era it has become increasingly apparent that the vast number of predicted biosynthesis genes of microorganisms is not reflected by the metabolic profile observed under standard fermentation conditions. In the absence of a particular (in most cases unknown) trigger these gene loci remain silent. Because these cryptic gene clusters may code for the biosynthesis of important virulence factors, toxins, or even drug candidates, new strategies for their activation are urgently needed to make use of this largely untapped reservoir of potentially bioactive compounds. The discovery of new microbial metabolites through genome mining has proven to be a very promising approach. Even so, the investigation of silent gene clusters is still a substantial challenge, particularly in fungi. Here we report a new strategy for the successful induction of a silent metabolic pathway in the important model organism Aspergillus nidulans, which led to the discovery of novel PKS-NRPS hybrid metabolites.

IFN-stimulated gene 15 functions as a critical antiviral molecule against influenza, herpes, and Sindbis viruses.

Abstract: Type I interferons (IFNs) play an essential role in the host response to viral infection through the induction of numerous IFN-stimulated genes (ISGs), including important antiviral molecules such as PKR, RNase L, Mx, and iNOS. Yet, additional antiviral ISGs likely exist. IFN-stimulated gene 15 (ISG15) is a ubiquitin homolog that is rapidly up-regulated after viral infection, and it conjugates to a wide array of host proteins. Although it has been hypothesized that ISG15 functions as an antiviral molecule, the initial evaluation of ISG15-deficient mice revealed no defects in their responses to vesicular stomatitis virus or lymphocytic choriomeningitis virus, leaving open the important question of whether ISG15 is an antiviral molecule in vivo. Here we demonstrate that ISG15 is critical for the host response to viral infection. ISG15−/− mice are more susceptible to influenza A/WSN/33 and influenza B/Lee/40 virus infections. ISG15−/− mice also exhibited increased susceptibility to both herpes simplex virus type 1 and murine gammaherpesvirus 68 infection and to Sindbis virus infection. The increased susceptibility of ISG15−/− mice to Sindbis virus infection was rescued by expressing wild-type ISG15, but not a mutant form of ISG15 that cannot form conjugates, from the Sindbis virus genome. The demonstration of ISG15 as a novel antiviral molecule with activity against both RNA and DNA viruses provides a target for the development of therapies against important human pathogens.

Aerosol-type-dependent lidar ratios observed with Raman lidar

Abstract: [1] We summarize our Raman lidar observations which were carried out in Europe, Asia, and Africa during the past 10 years, with focus on particle extinction-to-backscatter ratios (lidar ratios) and Angstrom exponents. For the first time, we present statistics on lidar ratios for almost all climatically relevant aerosol types solely based on Raman lidar measurements. Sources of continental particles were in North America and Europe, the Sahara, and south and Southeast and east Asia. The North Atlantic Ocean, and the tropical and South Indian Ocean were the sources of marine particles. The statistics are complemented with lidar ratios describing aged forest fire smoke and pollution from polar regions (Arctic haze) after long-range transport. In addition, we present particle Angstrom exponents for the wavelength range from 355 to 532 nm and from 532 to 1064 nm. We compare our data set of lidar ratios to the recently published AERONET (Aerosol Robotic Network) lidar ratio climatology. That climatology is based on aerosol scattering modeling in which AERONET Sun photometer observations serve as input. Raman lidar measurements of extinction-to-backscatter ratios of Saharan dust and urban aerosols differ significantly from the numbers obtained with AERONET Sun photometers. There are also differences for some of the Angstrom exponents. Further comparison studies are needed to reveal the reason for the observed differences.

A high density barley microsatellite consensus map with 775 SSR loci

Abstract: A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations ‘Igri × Franka’, ‘Steptoe × Morex’, ‘OWBRec × OWBDom’, ‘Lina × Canada Park’, ‘L94 × Vada’ and ‘SusPtrit × Vada’. Segregation data for microsatellite markers from different research groups including SCRI (Bmac, Bmag, EBmac, EBmag, HVGeneName, scsssr), IPK (GBM, GBMS), WUR (GBM), Virginia Polytechnic Institute (HVM), and MPI for Plant Breeding (HVGeneName), generated in above mapping populations, were used in the computer program RECORD to order the markers of the individual linkage data sets. Subsequently, a framework map was constructed for each chromosome by integrating the 496 “bridge markers” common to two or more individual maps with the help of the computer programme JoinMap® 3.0. The final map was calculated by following a “neighbours” map approach. The integrated map contained 775 unique microsatellite loci, from 688 primer pairs, ranging from 93 (6H) to 132 (2H) and with an average of 111 markers per linkage group. The genomic DNA-derived SSR marker loci had a higher polymorphism information content value (average 0.61) as compared to the EST/gene-derived SSR loci (average 0.48). The consensus map spans 1,068 cM providing an average density of one SSR marker every 1.38 cM. Such a high-density consensus SSR map provides barley molecular breeding programmes with a better choice regarding the quality of markers and a higher probability of polymorphic markers in an important chromosomal interval. This map also offers the possibilities of thorough alignment for the (future) physical map and implementation in haplotype diversity studies of barley.

Deletion of Complement Factor H–Related Genes CFHR1 and CFHR3 Is Associated with Atypical Hemolytic Uremic Syndrome

Abstract: Atypical hemolytic uremic syndrome (aHUS) is associated with defective complement regulation. Disease-associated mutations have been described in the genes encoding the complement regulators complement factor H, membrane cofactor protein, factor B, and factor I. In this study, we show in two independent cohorts of aHUS patients that deletion of two closely related genes, complement factor H–related 1 (CFHR1) and complement factor H–related 3 (CFHR3), increases the risk of aHUS. Amplification analysis and sequencing of genomic DNA of three affected individuals revealed a chromosomal deletion of ∼84 kb in the RCA gene cluster, resulting in loss of the genes coding for CFHR1 and CFHR3, but leaving the genomic structure of factor H intact. The CFHR1 and CFHR3 genes are flanked by long homologous repeats with long interspersed nuclear elements (retrotransposons) and we suggest that nonallelic homologous recombination between these repeats results in the loss of the two genes. Impaired protection of erythrocytes from complement activation is observed in the serum of aHUS patients deficient in CFHR1 and CFHR3, thus suggesting a regulatory role for CFHR1 and CFHR3 in complement activation. The identification of CFHR1/CFHR3 deficiency in aHUS patients may lead to the design of new diagnostic approaches, such as enhanced testing for these genes.

Metal nitride cluster fullerenes: their current state and future prospects.

Abstract: The world of endohedral fullerenes was significantly enlarged over the past seven years by the cluster fullerenes, which contain structures such as the M(2)C(2) carbides and the M(3)N nitrides. While the carbide clusters are generated under the standard arc-burning conditions according to stabilization conditions, the nitride cluster fullerenes (NCFs) are formed by varying the composition of the cooling gas atmosphere in the arc-burning process. The special conditions for NCF synthesis is described in detail and the optimum conditions for the production of NCFs as the main product in fullerene syntheses are given. A general review of all NCFs reported to date consists of the structures, properties, and stability of the NCFs as well as the abundance of the NCFs in the fullerene soot. It is shown that all cages with even carbon atoms from C(68) to C(98) are available as endohedral nitride cluster structures (with the exception of C(72), C(74), and C(76)). Specifically, the NCFs form the largest number of structures that violate the isolated pentagon rule (IPR). Finally some practical applications of these cluster fullerenes are illustrated and an outlook is given, taking the superior stability of these endohedral fullerenes into account.

Abnormal thyroid hormone metabolism in mice lacking the monocarboxylate transporter 8

Abstract: In humans, inactivating mutations in the gene of the thyroid hormone transporter monocarboxylate transporter 8 (MCT8; SLc16A2) lead to severe forms of psychomotor retardation combined with imbalanced thyroid hormone serum levels. The MCT8-null mice described here, however, developed without overt deficits but also exhibited distorted 3,5,3'-triiodothyronine (T3) and thyroxine (T4) serum levels, resulting in increased hepatic activity of type 1 deiodinase (D1). In the mutants' brains, entry of T4 was not affected, but uptake of T3 was diminished. Moreover, the T4 and T3 content in the brain of MCT8-null mice was decreased, the activity of D2 was increased, and D3 activity was decreased, indicating the hypothyroid state of this tissue. In the CNS, analysis of T3 target genes revealed that in the mutants, the neuronal T3 uptake was impaired in an area-specific manner, with strongly elevated thyrotropin-releasing hormone transcript levels in the hypothalamic paraventricular nucleus and slightly decreased RC3 mRNA expression in striatal neurons; however, cerebellar Purkinje cells appeared unaffected, since they did not exhibit dendritic outgrowth defects and responded normally to T3 treatment in vitro. In. conclusion, the circulating thyroid hormone levels of MCT8-null mice closely resemble those of humans with MCT8 mutations, yet in the mice, CNS development is only partially affected.

A new Saharan dust source activation frequency map derived from MSG-SEVIRI IR-channels

Abstract: We present a new dust source area map for the Sahara and Sahel region, derived from the spatiotemporal variability of composite images of Meteosat Second Generation (MSG) using the 87, 108 and 120 μm wavelength channels for March 2006–February 2007 Detected dust events have been compared to measured aerosol optical thickness (AOT) and horizontal visibility observations Furthermore the monthly source area map has been compared with the Ozone Monitoring Instrument aerosol index (AI) A spatial shift of the derived frequency patterns and the local maxima of AI-values can be explained by wind-transport of airborne dust implicitly included in the AI signal To illustrate the sensitivity of a regional model using the new dust source mask, we present a case study analysis that shows an improvement in reproducing aerosol optical thickness in comparison to the original dust source parameterization

Phytotoxicity and Innate Immune Responses Induced by Nep1-Like Proteins

Abstract: We show that oomycete-derived Nep1 (for necrosis and ethylene-inducing peptide1)–like proteins (NLPs) trigger a comprehensive immune response in Arabidopsis thaliana, comprising posttranslational activation of mitogen-activated protein kinase activity, deposition of callose, production of nitric oxide, reactive oxygen intermediates, ethylene, and the phytoalexin camalexin, as well as cell death. Transcript profiling experiments revealed that NLPs trigger extensive reprogramming of the Arabidopsis transcriptome closely resembling that evoked by bacteria-derived flagellin. NLP-induced cell death is an active, light-dependent process requiring HSP90 but not caspase activity, salicylic acid, jasmonic acid, ethylene, or functional SGT1a/SGT1b. Studies on animal, yeast, moss, and plant cells revealed that sensitivity to NLPs is not a general characteristic of phospholipid bilayer systems but appears to be restricted to dicot plants. NLP-induced cell death does not require an intact plant cell wall, and ectopic expression of NLP in dicot plants resulted in cell death only when the protein was delivered to the apoplast. Our findings strongly suggest that NLP-induced necrosis requires interaction with a target site that is unique to the extracytoplasmic side of dicot plant plasma membranes. We propose that NLPs play dual roles in plant pathogen interactions as toxin-like virulence factors and as triggers of plant innate immune responses.

New particle formation in Beijing, China: Statistical analysis of a 1‐year data set

Abstract: [1] Particle number size distributions between 3 nm and 10 μm were measured in Beijing, China. New particle formation events were observed on around 40% of the measurement days from March 2004 to February 2005 and were generally observed under low relative humidity and sunny conditions. Though occurring during all seasons, new particle formation events had highest frequency in spring and lowest frequency in summer. Events were classified as “clean” or “polluted” groups mainly according to the condensational sink and the local wind. The formation rate range was from 3.3 to 81.4 cm−3 s−1. The growth rate varied from 0.1 to 11.2 nm h−1. The seasonal variation of condensable vapor concentration showed the highest values during summer months due to enhanced photochemical and biological activities as well as stagnant air masses preventing exchange with cleaner air.

Why are cooperatives important in agriculture? An organizational economics perspective

Abstract: This paper develops an organizational economics explanation for agricultural cooperatives by building upon the transaction cost theory of family farms. According to this theory, the importance of family farms in Western agriculture is a result of the low feasibility of hierarchical organization in agricultural production due to supervision and monitoring difficulties. This paper argues that the transaction cost-economizing effect of family farms has a price in the form of their limited ability to realize economies of scale and to develop market power comparable to that of their up- and downstream trading partners. The role of agricultural cooperatives is shown to help overcome these limitations in order to take advantage of the transaction-cost economizing properties of family farms. This explanation of agricultural cooperatives is sector-specific in the sense that it traces the benefits of cooperative organization back to the organizational attributes of agricultural production.

A Novel Transcriptional Cascade Regulating Expression of Heat Stress Proteins during Seed Development of Arabidopsis

Abstract: Within the Arabidopsis thaliana family of 21 heat stress transcription factors (Hsfs), HsfA9 is exclusively expressed in late stages of seed development. Here, we present evidence that developmental expression of HsfA9 is regulated by the seed-specific transcription factor ABSCISIC ACID–INSENSITIVE3 (ABI3). Intriguingly, ABI3 knockout lines lack detectable levels of HsfA9 transcript and protein, and further ectopic expression of ABI3 conferred the ability to accumulate HsfA9 in response to abscisic acid in transgenic plantlets. Consequently, the most abundant heat stress proteins (Hsps) in seeds (Hsp17.4-CI, Hsp17.7-CII, and Hsp101) were not detectable in the ABI3 knockout lines, but their expression could be detected in plants ectopically expressing HsfA9 in vegetative tissues. Furthermore, this seed-specific transcription factor cascade was reconstructed in transient β-glucuronidase reporter assays in mesophyll protoplasts by showing that ABI3 could activate the HsfA9 promoter, whereas HsfA9 in turn was shown to be a potent activator on the promoters of Hsp genes. Thus, our study establishes a genetic framework in which HsfA9 operates as a specialized Hsf for the developmental expression of Hsp genes during seed maturation.

Corrosion and related mechanical properties of bulk metallic glasses

Abstract: The review of corrosion performance of a number of alloy systems documents several metallic glasses with corrosion resistance superior to that of crystalline metals. In other cases, the metallic glasses do not have superior corrosion resistance. The nature of corrosion resistance of the metallic glasses is often directly related to the development of a passive film (protective layer) on the reactive alloy substrate, increased durability of the passive film, or enhanced resistance to localized corrosion where the passive film is broken or damaged. Potential mechanical/environmental degradation processes include stress-corrosion cracking, corrosion fatigue, various forms of hydrogen damage, wear, and abrasion. The availability of bulk metallic glasses in significant three-dimensional sizes will stimulate important work in these areas that will enhance the fundamental understanding of the corrosion behavior and mechanical interactions and develop design guidelines and materials properties database for designers and engineers.

Current strategies towards hemocompatible coatings

Abstract: A wide range of biomedical devices is applied clinically in contact with blood. Tailoring the surface properties of the involved biomaterials is a common approach to enhance performance and to limit adverse reactions. This review summarizes current trends in coating technologies developed for that purpose. Inorganic coatings were shown to substantially improve the durability and inertness of biomaterials while a number of advanced polymer coatings were demonstrated to be very effective by targeting specific biochemical pathways. However, to fully utilize the power of these bioactive coatings safety issues need to be thoroughly addressed in future studies.

Climate change affects timing and size of populations of an invasive cyanobacterium in temperate regions.

Abstract: Cylindrospermopsis raciborskii, an invasive freshwater cyanobacterium, originated from the tropics but has spread to temperate zones over the last few decades. Its northernmost populations in Europe occur in North German lakes. How such dramatic changes in its biogeography are possible and how its population dynamics in the newly invaded habitats are regulated are still unexplained. We therefore conducted a long-term (1993–2005) study of two German lakes to elucidate the mechanisms behind C. raciborskii population dynamics and to identify the abiotic constraints on its development. Our data revealed that pelagic populations of C. raciborskii thrived for three months during the summer, contributing up to 23% of the total cyanobacteria biovolume. Population sizes varied greatly between years without exhibiting any distinct long-term trends. In the annual lifecycle, C. raciborskii filaments emerged in the pelagic habitat when the temperature rose above 15–17 °C. At that time, mean photosynthetically active radiation in the mixed water column (Imix) overstepped its maximum. Rates of population net increase were highest at the beginning of the season (0.15–0.28 day−1), declined continuously over time, and were significantly positively correlated with Imix. This indicates that the onset of the pelagic population is temperature-mediated and that Imix controls its growth. Since Imix peaks before the population onset, the time of germination is of crucial importance for successful development. To test this hypothesis, we designed a model to simulate pelagic population size, starting at different dates in the annual cycle. Moving the population onset forward by 30 days resulted in a doubling of the population size. We therefore conclude that an earlier rise in water temperature associated with climate change has promoted the spread of C. raciborskii to the temperate zone. Earlier warming permits earlier germination, thereby shifting the pelagic populations to a phase with higher Imix, which advances growth and the population establishment.

A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics

Abstract: An integrated barley transcript map (consensus map) comprising 1,032 expressed sequence tag (EST)-based markers (total 1,055 loci: 607 RFLP, 190 SSR, and 258 SNP), and 200 anchor markers from previously published data, has been generated by mapping in three doubled haploid (DH) populations. Between 107 and 179 EST-based markers were allocated to the seven individual barley linkage groups. The map covers 1118.3 cM with individual linkage groups ranging from 130 cM (chromosome 4H) to 199 cM (chromosome 3H), yielding an average marker interval distance of 0.9 cM. 475 EST-based markers showed a syntenic organisation to known colinear linkage groups of the rice genome, providing an extended insight into the status of barley/rice genome colinearity as well as ancient genome duplications predating the divergence of rice and barley. The presented barley transcript map is a valuable resource for targeted marker saturation and identification of candidate genes at agronomically important loci. It provides new anchor points for detailed studies in comparative grass genomics and will support future attempts towards the integration of genetic and physical mapping information.

Selenium in chemistry and biochemistry in comparison to sulfur.

Abstract: What makes selenoenzymes--seen from a chemist's view--so special that they cannot be substituted by just more analogous or adapted sulfur proteins? This review compiles and compares physicochemical properties of selenium and sulfur, synthetic routes to selenocysteine (Sec) and its peptides, and comparative studies of relevant thiols and selenols and their (mixed) dichalcogens, required to understand the special role of selenium in selenoproteins on the atomic molecular level. The biochemically most relevant differences are the higher polarizability of Se- and the lower pKa of SeH. The latter has a strikingly different pH-dependence than thiols, with selenols being active at much lower pH. Finally, selected typical enzymatic mechanisms which involve selenocysteine are critically discussed, also in view of the authors' own results.

Impact of summer warming on the thermal characteristics of a polymictic lake and consequences for oxygen, nutrients and phytoplankton

Abstract: Summary 1. The impact of long thermal stratification events on some key properties in a polymictic lake was studied by determining the mixing regime of Muggelsee, Germany, using water temperature profiles taken hourly over 4 years. The period included two exceptional summer heatwaves. 2. Long thermal stratification events lasted from about 1 week to 2 months, and exhibited a high variability in thermocline depth and stratification intensity within and between events. 3. During stratification events, hypolimnetic oxygen concentrations strongly decreased while hypolimnetic SRP accumulation increased, depending on the duration and intensity of stratification and on hypolimnetic water temperature. 4. The impact of stratification on the functional phytoplankton composition increased with increasing stratification duration, but was rather different for the heatwaves. 5. Stratification events were followed by strong nutrient pulses into the euphotic zone and intense phytoplankton growth, particularly after the heatwaves. Hence, the influence of the climate extremes counteracted effects of reduced external nutrient loading.