Conserved intron positions in ancient protein modules

Background  

The timing of the origin of introns is of crucial importance for an understanding of early genome architecture. The Exon theory of genes proposed a role for introns in the formation of multi-exon proteins by exon shuffling and predicts the presence of conserved splice sites in ancient genes. In this study, large-scale analysis of potential conserved splice sites was performed using an intron-exon database (ExInt) derived from GenBank.     

Application of NHG guidelines in patients referred for stable chest pain syndromes

Purpose. Guidelines of the Dutch Association of General Practitioners (NHG) dictate the evaluation, treatment, and referral process of patients with stable chest pain syndromes (CPS). Adherence to this guideline was assessed in a consecutive group of patients referred to our hospital. Methods. We retrospectively studied the records of 296 subjects referred to our outpatient department in 2007 for evaluation of stable CPS. Referral letters were checked for completeness (past and present history, mentioning of risk factors for cardiovascular disease, physical examination, listing of medication) and used to judge adherence to the guideline. In a subset of patients, additional information regarding the referral process was gathered by telephone interview. Results. The referral letter was complete in only 67 patients (23%); items most often not reported were physical examination (63%) and cardiovascular risk factors (62%). Judging from the referral letter, 23 patients (8%) were evaluated in accordance with the NHG guideline prior to their referral. In patients in whom the final diagnosis of angina pectoris was made by the cardiologist, this was 20%. Seventy-nine patients were contacted by telephone after their work-up by the cardiologist; 36 of them (44%) reported being referred at their first visit to their primary physician, while 14 (18%) were referred at their own request. Conclusion: Prior to referral, only a minority of patients with stable CPS were evaluated and treated in accordance with NHG guidelines. Furthermore, their referral letter was often incomplete. (Neth Heart J 2010;18:178-82.)     

Unique genomic configuration revealed by microsatellite DNA in polyploid dogroses, Rosa sect. Caninae

An allopolyploid complex with high genomic integrity has been studied. Dogroses transmit only seven chromosomes (from seven bivalents) through the pollen, whereas 21, 28 or 35 chromosomes (from seven bivalents and 14, 21 or 28 univalents) come from the egg cells. Seedlings derived from two interspecific crosses were analysed with flow cytometry and molecular markers to determine ploidy level, mode of reproduction and genomic constitution. Evidence was obtained for the formation of unreduced male and female gametes, which can take part in fertilization (producing seedlings with higher ploidy than the parental plants) or in apomictic reproduction. Random amplified polymorphic DNA (RAPD) and microsatellite analyses indicated that three seedlings (5%) were derived through apomixis, whereas the other 49 were hybrids. Bivalent formation appears to involve chromosomes that consistently share the same microsatellite alleles. Allele-sharing between the maternally transmitted and highly conserved univalent-forming chromosomes reflected the taxonomic distance between different genotypes. The frequently recombining bivalent-forming chromosomes were taxonomically less informative.     

Sepsis progression and outcome: a dynamical model

Background  

Sepsis (bloodstream infection) is the leading cause of death in non-surgical intensive care units. It is diagnosed in 750,000 US patients per annum, and has high mortality. Current understanding of sepsis is predominately observational and correlational, with only a partial and incomplete understanding of the physiological dynamics underlying the syndrome. There exists a need for dynamical models of sepsis progression, based upon basic physiologic principles, which could eventually guide hourly treatment decisions.     

Moorland pools as refugia for endangered species characteristic of raised bog gradients

In intact raised bog landscapes transitions from ombrotrophic into minerotrophic conditions occur. These gradients are lost from many bogs due to peat harvesting and drainage, and are difficult to restore. To determine which endangered species are characteristic of pristine raised bog gradients and their current status in degraded bogs, plants and macroinvertebrates were surveyed in Estonian intact raised bogs and Dutch degraded bog remnants. Dutch national distribution data were used to determine whether communities with these species occurred outside bog habitats. Water chemistry data were used to describe associated environmental conditions. Intact bog gradients were the preferred habitat for six plant species and fifteen macroinvertebrate species, all of which are endangered. In degraded bogs these species were scarce or not recorded. In intact bogs these species lived at sites where runoff from the bog massif came into contact with regional ground water resulting in a gradient in pH, alkalinity, Ca, Fe and ionic ratio. Analysis of Dutch national distribution data revealed aggregations of these endangered species in moorland pools. These pools contained water chemistry gradients similar to those found in pristine bogs, which occurred at sites were groundwater seepage and stream water came in contact. In the past, stream water has been used to increase pH and trophic status of moorland pools facilitating fisheries. Today, this practice offers a conservation strategy for the protection of endangered species for which no short-term alternatives are available.     

Do restoration measures rehabilitate fauna diversity in raised bogs? A comparative study on aquatic macroinvertebrates

To assess whether raised bog restorationmeasures contribute to the conservation andrestoration of the fauna diversity,macroinvertebrate species assemblages werecompared between water bodies created byrewetting measures and water bodies whichhave not been subject to restorationmeasures, but are remnants offormer peat cuttings and trenches used forbuckwheat culture in the past.The restoration sites were inhabited bycharacteristic raised bog species and rarespecies, but their numbers were higher atthe remnant sites not affected byrestoration management. A considerablenumber of characteristic and rare faunaspecies were only found at the remnantsites. The remnant sites includedconsiderably more variation inmacroinvertebrate species assemblages andhad a higher cumulative species richness.The number of characteristicmacroinvertebrate species was not clearlyrelated to the presence of a characteristicraised bog vegetation. In restoration sitesnumbers of rare and characteristic speciesper site tended to increase with the timeelapsed after rewetting. However,restoration measures will not automaticallyresult in restoration of a more or lesscomplete macroinvertebrate speciesspectrum, as restoration measures have sofar resulted in habitats for only a limitednumber of the characteristic species.When planning restoration measures, it isrecommended to protect the populations ofrare and characteristic species present inthe area, as these populations may becomethe sources for colonization of rewettedsites. Safeguarding habitat diversityduring the restoration process andrestoration of different elements of thehabitat diversity of complete raised bogsystems will result in the characteristicfauna diversity being conserved andrestored more successfully.     

Partial preferential chromosome pairing is genotype dependent in tetraploid rose

It has long been recognised that polyploid species do not always neatly fall into the categories of auto‐ or allopolyploid, leading to the term ‘segmental allopolyploid’ to describe everything in between. The meiotic behaviour of such intermediate species is not fully understood, nor is there consensus as to how to model their inheritance patterns. In this study we used a tetraploid cut rose (Rosa hybrida) population, genotyped using the 68K WagRhSNP array, to construct an ultra‐high‐density linkage map of all homologous chromosomes using methods previously developed for autotetraploids. Using the predicted bivalent configurations in this population we quantified differences in pairing behaviour among and along homologous chromosomes, leading us to correct our estimates of recombination frequency to account for this behaviour. This resulted in the re‐mapping of 25 695 SNP markers across all homologues of the seven rose chromosomes, tailored to the pairing behaviour of each chromosome in each parent. We confirmed the inferred differences in pairing behaviour among chromosomes by examining repulsion‐phase linkage estimates, which also carry information about preferential pairing and recombination. Currently, the closest sequenced relative to rose is Fragaria vesca. Aligning the integrated ultra‐dense rose map with the strawberry genome sequence provided a detailed picture of the synteny, confirming overall co‐linearity but also revealing new genomic rearrangements. Our results suggest that pairing affinities may vary along chromosome arms, which broadens our current understanding of segmental allopolyploidy.     

A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants

Background

Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity.

Results

To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363 NB-LRR genes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem- (mean = 1.59), ohnolog (mean = 1.36) and singleton (mean = 1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 NB-LRR genes present in the model plant Arabidopsis and describe four distinct clusters of NB-LRR “gatekeeper” loci sharing syntenic orthologs across all analyzed genomes.

Conclusion

By curating a near-complete set of multi-domain R-protein clusters in an eudicot-wide scale, our analysis offers significant insight into evolutionary dynamics underlying diversification of the plant innate immune system. Furthermore, our methods provide a blueprint for future efforts to identify and more rapidly clone functional NB-LRR genes from any plant species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-966) contains supplementary material, which is available to authorized users.