Interleukin-1 stimulates prostaglandin biosynthesis by human amnion

The purpose of these studies was to determine if Interleukin-1 (IL-1) alters the rate of prostaglandin biosynthesis by human amnion. Primary monolayer cultures of amnion cells were established from women undergoing elective cesarean section before the onset of labor. Natural purified and recombinant human IL-1 alpha and IL-1 beta were incubated with amnion cells in culture, and prostaglandin E2 (PGE2) biosynthesis was measured by radioimmunoassay in cell-free media. A concentration-dependent increase in PGE2 production by amnion cells occurred in response to natural purified and recombinant IL-1 preparations. No differences in the parameters of the dose-response curves between the two IL-1 gene products could be determined (p greater than 0.05). Indomethacin blocked the effect of IL-1 in prostaglandin biosynthesis by human amnion. Interleukin-1, a fever mediator, could serve as a signal for the initiation of labor in cases of intrauterine or systemic infection.     

Bacterial endotoxin and tumor necrosis factor stimulate prostaglandin production by human decidua

The purpose of these studies was to determine the effect of bacterial endotoxin and tumor necrosis factor (TNF) on prostaglandin (PG) secretion by human decidua. Decidual explants were established from women undergoing elective cesarean sections before the onset of labor. Escherichia Coli endotoxin and purified human recombinant TNF (rh TNF) were incubated with decidual explants. PGF2 alpha and PGE2 biosynthesis was measured by radioimmunoassay. A significant increase in the release of all PGs into the media occurred in response to LPS and TNF. In the setting of an extraamniotic infection, bacterial and host secretory products (TNF) could trigger the onset of labor, activating the decidua to produce PGs.     

A high density physical map of chromosome 1BL supports evolutionary studies,map-based cloning and sequencing in wheat

Background

As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning.

Results

Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome.

Conclusions

Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing.     

Evaluation and classification of RING-finger domains encoded by the <Emphasis Type="Italic">Arabidopsis</Emphasis> genome

Background

In computational analysis, the RING-finger domain is one of the most frequently detected domains in the Arabidopsis proteome. In fact, it is more abundant in Arabidopsis than in other eukaryotic genomes. However, computational analysis might classify ambiguous domains of the closely related PHD and LIM motifs as RING domains by mistake. Thus, we set out to define an ordered set of Arabidopsis RING domains by evaluating predicted domains on the basis of recent structural data.

Results

Inspection of the proteome with a current InterPro release predicts 446 RING domains. We evaluated each detected domain and as a result eliminated 59 false positives. The remaining 387 domains were grouped by cluster analysis and according to their metal-ligand arrangement. We further defined novel patterns for additional computational analyses of the proteome. They were based on recent structural data that enable discrimination between the related RING, PHD and LIM domains. These patterns allow us to predict with different degrees of certainty whether a particular domain is indeed likely to form a RING finger.

Conclusions

In summary, 387 domains have a significant potential to form a RING-type cross-brace structure. Many of these RING domains overlap with predicted PHD domains; however, the RING domain signature mostly prevails. Thus, the abundance of PHD domains in Arabidopsis has been significantly overestimated. Cluster analysis of the RING domains defines groups of proteins, which frequently show significant similarity outside the RING domain. These groups document a common evolutionary origin of their members and potentially represent genes of overlapping functionality.

     

Computerized equipment to control soil water matric potential and soil temperature in inoculum potential assays of soil-borne pathogens

Computerized equipment to control soil temperature and soil water matric potential, at high soil hydric conditions was developed and evaluated. A series of experiments demonstrated the accuracy and reproducibility of the equipment's performance and its adequacy for the assessment of the inoculum potential of soil-borne pathogens in soils with different characteristics. Control of soil water potential is achieved by variation in the height of the water table in a medium with high water conductivity supporting the soil. The equipment consists of double-walled tanks, permitting the adjustment of soil temperature. It is provided with sensors, control software and valves for automatic operation. in a growth chamber at 24°C. with RH 70% and irradiation of 90 W.m^–2, was maintained in dynamic equilibrium for pF values ranging from 1 (–1 kPa) to 2 (–10 kPa) in various arable soil samples during the four to five weeks period of the bioassays. During the fourth week of pea or iris growth at pF=2, the system controlled within an amplitude of 0.4 pF-units. Between replications, variance was approximately 0.1 at F=2, decreasing with increasing. Soil temperature in the system could be maintained at a constant level with a variance below 0.1, within an amplitude of 0.3°C.     

The attractiveness of the Droop equations.

The Droop equations are a system of three coupled, nonlinear ordinary differential equations describing the growth of a microorganism in a chemostat. The growth rate of the organism is limited by the availability of a single nutrient. In contrast to the better known Monod equations, the nutrient is divided into external and internal cellular pools. Only the internal pool can catalyze growth. This paper proves that the Droop equations are globally stable. Based on a single combination of parameters, either the chemostat organism goes extinct or it tends to a fixed, positive concentration.     

Distribution,functional impact,and origin mechanisms of copy number variation in the barley genome

Background

There is growing evidence for the prevalence of copy number variation (CNV) and its role in phenotypic variation in many eukaryotic species. Here we use array comparative genomic hybridization to explore the extent of this type of structural variation in domesticated barley cultivars and wild barleys.

Results

A collection of 14 barley genotypes including eight cultivars and six wild barleys were used for comparative genomic hybridization. CNV affects 14.9% of all the sequences that were assessed. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. CNVs are enriched near the ends of all chromosomes except 4H, which exhibits the lowest frequency of CNVs. CNV affects 9.5% of the coding sequences represented on the array and the genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases. Sequence-based comparisons of CNV between cultivars Barke and Morex provided evidence that DNA repair mechanisms of double-strand breaks via single-stranded annealing and synthesis-dependent strand annealing play an important role in the origin of CNV in barley.

Conclusions

We present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley, and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance. We also identify potential mechanisms that can generate variation in copy number in plant genomes.