Spatial Genetic Structure of the Abundant and Widespread Peatmoss Sphagnum magellanicum Brid.

Spore-producing organisms have small dispersal units enabling them to become widespread across continents. However, barriers to gene flow and cryptic speciation may exist. The common, haploid peatmoss Sphagnum magellanicum occurs in both the Northern and Southern hemisphere, and is commonly used as a model in studies of peatland ecology and peatmoss physiology. Even though it will likely act as a rich source in functional genomics studies in years to come, surprisingly little is known about levels of genetic variability and structuring in this species. Here, we assess for the first time how genetic variation in S. magellanicum is spatially structured across its full distribution range (Northern Hemisphere and South America). The morphologically similar species S. alaskense was included for comparison. In total, 195 plants were genotyped at 15 microsatellite loci. Sequences from two plastid loci (trnG and trnL) were obtained from 30 samples. Our results show that S. alaskense and almost all plants of S. magellanicum in the northern Pacific area are diploids and share the same gene pool. Haploid plants occur in South America, Europe, eastern North America, western North America, and southern Asia, and five genetically differentiated groups with different distribution ranges were found. Our results indicate that S. magellanicum consists of several distinct genetic groups, seemingly with little or no gene flow among them. Noteworthy, the geographical separation of diploids and haploids is strikingly similar to patterns found within other haploid Sphagnum species spanning the Northern Hemisphere. Our results confirm a genetic division between the Beringian and the Atlantic that seems to be a general pattern in Sphagnum taxa. The pattern of strong genetic population structuring throughout the distribution range of morphologically similar plants need to be considered in future functional genomic studies of S. magellanicum.     

Whole Genome Gene Expression Meta-Analysis of Inflammatory Bowel Disease Colon Mucosa Demonstrates Lack of Major Differences between Crohn's Disease and Ulcerative Colitis

Background

In inflammatory bowel disease (IBD), genetic susceptibility together with environmental factors disturbs gut homeostasis producing chronic inflammation. The two main IBD subtypes are Ulcerative colitis (UC) and Crohn’s disease (CD). We present the to-date largest microarray gene expression study on IBD encompassing both inflamed and un-inflamed colonic tissue. A meta-analysis including all available, comparable data was used to explore important aspects of IBD inflammation, thereby validating consistent gene expression patterns.

Methods

Colon pinch biopsies from IBD patients were analysed using Illumina whole genome gene expression technology. Differential expression (DE) was identified using LIMMA linear model in the R statistical computing environment. Results were enriched for gene ontology (GO) categories. Sets of genes encoding antimicrobial proteins (AMP) and proteins involved in T helper (Th) cell differentiation were used in the interpretation of the results. All available data sets were analysed using the same methods, and results were compared on a global and focused level as t-scores.

Results

Gene expression in inflamed mucosa from UC and CD are remarkably similar. The meta-analysis confirmed this. The patterns of AMP and Th cell-related gene expression were also very similar, except for IL23A which was consistently higher expressed in UC than in CD. Un-inflamed tissue from patients demonstrated minimal differences from healthy controls.

Conclusions

There is no difference in the Th subgroup involvement between UC and CD. Th1/Th17 related expression, with little Th2 differentiation, dominated both diseases. The different IL23A expression between UC and CD suggests an IBD subtype specific role. AMPs, previously little studied, are strongly overexpressed in IBD. The presented meta-analysis provides a sound background for further research on IBD pathobiology.     

Refractions through culture: the new genomics in Iceland

This paper explores the processes whereby complex scientific developments are rendered into locally intelligible idioms as part of strategies to incorporate a ‘public’ in decisions which may have profound implications in the longer term. We focus in particular on the recent developments in genetic technologies and take as our example the deCode biogenetic project in Iceland. We trace how the images and metaphors drawn upon by all sides of the debate created powerful resonances with Icelandic history and culture. We analyse these representations and the broader themes of ethnicity and nationalism which they invoke.     

Prevention of ischemic ventricular tachycardia of Purkinje origin: role for alpha(2)-adrenoceptors in Purkinje?

Recent studies have shown the presence of postjunctional alpha(2)-adrenergic receptors on canine Purkinje fibers but not muscle cells. Stimulation of these receptors results in prolongation of the action potential duration and the Purkinje relative refractory period. We studied the effect of alpha(2)-adrenergic agonists on inducible ischemic ventricular tachycardia (VT) of both Purkinje fiber and myocardial origin. Open-chest dogs in whom VT was induced with extrastimuli after occlusion of the anterior descending coronary artery were studied. A mapping system, incorporating Purkinje signals, characterized the mechanisms of VT. The alpha(2)-adrenergic agonists clonidine (0.5-4.0 microg/kg) or UK 14,304 (4-5 microg/kg) versus saline were given intravenously after reproducibility of inducible sustained monomorphic VT had been demonstrated. Eighteen dogs were given clonidine, eleven of which had focal Purkinje VT. Of these 11 dogs, clonidine blocked VT induction in 9 (81.9%) and rendered VT nonsustained in 1 (9.1%), and VT remained inducible in 1 dog (9.1%), although this was focal midmyocardial VT only. In the seven dogs with VT of myocardial origin, six (85.6%) remained inducible with clonidine, whereas one dog (14.4%) had only nonsustained VT after clonidine. Of the six dogs, UK 14,304 blocked VT induction in four (66.6%) and rendered VT nonsustained in one (16.7%), and VT remained inducible in one dog (16.7%). In four dogs with VT of myocardial origin, VT remained inducible. In the eight control dogs that were given saline, focal Purkinje VT was repeatedly inducible. Pharmacological stimulation of postjunctional alpha(2)-adrenoceptors on Purkinje fibers may selectively prevent induction of VT of Purkinje fiber origin in the ischemic canine ventricle.     

Origin, taxonomy and population structure of the allopolyploid peat mossSphagnum majus

The polyploid peat mossSphagnum majus shows considerable phenotypic plasticity along ecological gradients in mires. It is considered taxonomically heterogeneous, and two subspecies have been described. Isozyme analyses were carried out on populations ofS. majus from Central Norway and from eastern coast of North America in order to assess the origin, taxonomy and population structure of this species. High levels of fixed heterozygosity in the populations demonstrate thatS. majus is a genetic allopolyploid. At all loci screened, extant populations ofS. cuspidatum shared enzyme bands withS. majus. The other most likely progenitor based on morphology,S. annulatum, was fixed for enzyme bands not found inS. majus. The progenitor genotype ofS. annulatum may have been missed because of inadequate sampling or extinction. Alternatively, another extinct or undetected taxon may constitute the second progenitor. The observed patterns of genetic variation and linkage disequilibria were uncorrelated with the previously proposed subspecific classification ofS. majus. Lack of genetic divergence between continents suggests that the origins ofS. majus in Europe and North America were not independent. Low mutation rates and large effective population sizes may be important causing populations to diverge slowly, and may explain the observed patterns without hypothesising frequent long-distance dispersal.     

Trans-Atlantic genetic uniformity in the rare snowbed sedge <Emphasis Type="Italic">Carex rufina</Emphasis>

The red-listed, amphi-Atlantic sedge Carex rufina is highly specialized to certain alpine snowbeds, and threatened by current changes in snow cover duration and moisture conditions. Here we address its range-wide genetic diversity, history, and conservation using amplified fragment length polymorphisms (AFLPs). Despite extensive primer testing, we detected very low overall diversity (4.1% polymorphic markers). Only a single AFLP phenotype was found throughout Norway and across the Atlantic to Iceland and Greenland, while another was found in Canada, suggesting glacial survival in one East and one West Atlantic refugium. East Atlantic C. rufina has probably been heavily bottlenecked in a small refugium, possibly situated within the maximum limits of the ice sheets. Its lack of diversity is likely maintained through local clonal growth causing longevity of genotypes. Habitat availability appears as the main limiting factor for C. rufina, and its currently occupied habitats need to be preserved to ensure its long-time survival.     

Functional evolution of a cis-regulatory module

Lack of knowledge about how regulatory regions evolve in relation to their structure–function may limit the utility of comparative sequence analysis in deciphering cis-regulatory sequences. To address this we applied reverse genetics to carry out a functional genetic complementation analysis of a eukaryotic cis-regulatory module—the even-skipped stripe 2 enhancer—from four Drosophila species. The evolution of this enhancer is non-clock-like, with important functional differences between closely related species and functional convergence between distantly related species. Functional divergence is attributable to differences in activation levels rather than spatiotemporal control of gene expression. Our findings have implications for understanding enhancer structure–function, mechanisms of speciation and computational identification of regulatory modules.     

Uracil-DNA glycosylase in base excision repair and adaptive immunity: species differences between man and mouse

Genomic uracil is a DNA lesion but also an essential key intermediate in adaptive immunity. In B cells, activation-induced cytidine deaminase deaminates cytosine to uracil (U:G mispairs) in Ig genes to initiate antibody maturation. Uracil-DNA glycosylases (UDGs) such as uracil N-glycosylase (UNG), single strand-selective monofunctional uracil-DNA glycosylase 1 (SMUG1), and thymine-DNA glycosylase remove uracil from DNA. Gene-targeted mouse models are extensively used to investigate the role of these enzymes in DNA repair and Ig diversification. However, possible species differences in uracil processing in humans and mice are yet not established. To address this, we analyzed UDG activities and quantities in human and mouse cell lines and in splenic B cells from Ung(+/+) and Ung(-/-) backcrossed mice. Interestingly, human cells displayed ～15-fold higher total uracil excision capacity due to higher levels of UNG. In contrast, SMUG1 activity was ～8-fold higher in mouse cells, constituting ～50% of the total U:G excision activity compared with less than 1% in human cells. In activated B cells, both UNG and SMUG1 activities were at levels comparable with those measured for mouse cell lines. Moreover, SMUG1 activity per cell was not down-regulated after activation. We therefore suggest that SMUG1 may work as a weak backup activity for UNG2 during class switch recombination in Ung(-/-) mice. Our results reveal significant species differences in genomic uracil processing. These findings should be taken into account when mouse models are used in studies of uracil DNA repair and adaptive immunity.     

Genetic analysis of four Île Amsterdam Sphagna: high morphological divergence within Sphagnum subgenus Subsecunda

This study uses microsatellites (SSRs) and nucleotide sequences to explore unresolved questions associated with four of the six Sphagnum species reported for Île Amsterdam: Sphagnum cavernulosum of unknown subgenus, S. complanatum and S. islei of subg. Subsecunda, and plants that initial morphological study placed in subg. Cuspidata. Genetic analyses show that all four species belong to subgenus Subsecunda and that none are allopolyploids. The plants initially placed in subg. Cuspidata are shown to belong to the ‘S. africanum’ clade of subg. Subsecunda and are closest to the African S. truncatum based on morphology. Sphagnum cavernulosum, S. complanatum, and S. islei are part of the Afro-Australasian clade of subg. Subsecunda, with S. complanatum and S. islei being closely associated with the African ‘S. capense’ complex and S. cavernulosum, which is morphologically divergent from all extant subgenera in the genus, being an outlier within this clade. Preliminary genetic analyses show S. islei to be closely related to S. complanatum and that they may represent two morphologically divergent genets of one species. The ancestral origins for the Île Amsterdam populations of S. complanatum, S. islei, and S. cf. truncatum are each ultimately based in Africa. Further study is required to determine the ecological and evolutionary significance, if any, provided by the pronounced morphological variation within species and the high morphological divergence among species in subg. Subsecunda. Finally, a prior report of S. recurvum (subg. Cuspidata) possibly occurring on Île Amsterdam is concluded to have been based on laboratory error.     

High genetic diversity in a remote island population system: sans sex

It has been proposed that long-distance dispersal of mosses to the Hawaiian Islands rarely occurs and that the Hawaiian population of the allopolyploid peat moss Sphagnum palustre probably resulted from a single dispersal event. Here, we used microsatellites to investigate whether the Hawaiian population of the dioicous S. palustre had a single founder and to compare its genetic diversity to that found in populations of S. palustre in other regions. The genetic diversity of the Hawaiian population is comparable to that of larger population systems. Several lines of evidence, including a lack of sporophytes and an apparently restricted natural distribution, suggest that sexual reproduction is absent in the Hawaiian plants. In addition, all samples of Hawaiian S. palustre share a genetic trait rare in other populations. Time to most recent ancestor (TMRCA) analysis indicates that the Hawaiian population was probably founded 49-51 kyr ago. It appears that all Hawaiian plants of S. palustre descend from a single founder via vegetative propagation. The long-term viability of this clonal population coupled with the development of significant genetic diversity suggests that vegetative propagation in a moss does not necessarily preclude evolutionary success in the long term.