Nucleotide variation at the CHALCONE ISOMERASE locus in Arabidopsis thaliana

An approximately 1.9-kb region encompassing the CHI gene, which encodes chalcone isomerase, was sequenced in 24 worldwide ecotypes of Arabidopsis thaliana (L.) Heynh. and in 1 ecotype of A. lyrata ssp. petraea. There was no evidence for dimorphism at the CHI region. A minimum of three recombination events was inferred in the history of the sampled ecotypes of the highly selfing A. thaliana. The estimated nucleotide diversity theta(TOTAL) = 0.004, theta(SIL) = 0. 005 was on the lower part of the range of the corresponding estimates for other gene regions. The skewness of the frequency spectrum toward an excess of low-frequency polymorphisms, together with the bell-shaped distribution of pairwise nucleotide differences at CHI, suggests that A. thaliana has recently experienced a rapid population growth. Although this pattern could also be explained by a recent selective sweep at the studied region, results from the other studied loci and from an AFLP survey seem to support the expansion hypothesis. Comparison of silent polymorphism and divergence at the CHI region and at the Adh1 and ChiA revealed in some cases a significant deviation of the direct relationship predicted by the neutral theory, which would be compatible with balancing selection acting at the latter regions.     

Studying genetics of adaptive variation in model organisms: flowering time variation in Arabidopsis lyrata

Arabidopsis thaliana has emerged as a model organism for plant developmental genetics, but it is also now being widely used for population genetic studies. Outcrossing relatives of A. thaliana are likely to provide suitable additional or alternative species for studies of evolutionary and population genetics. We have examined patterns of adaptive flowering time variation in the outcrossing, perennial A. lyrata. In addition, we examine the distribution of variation at marker genes in populations form North America and Europe. The probability of flowering in this species differs between southern and northern populations. Northern populations are much less likely to flower in short than in long days. A significant daylength by region interaction shows that the northern and southern populations respond differently to the daylength. The timing of flowering also differs between populations, and is made shorter by long days, and in some populations, by vernalization. North American and European populations show consistent genetic differentiation over microsatellite and isozyme loci and alcohol dehydrogenase sequences. Thus, the patterns of variation are quite different from those in A. thaliana, where flowering time differences show little relationship to latitude of origin and the genealogical trees of accessions vary depending on the genomic region studied. The genetic architecture of adaptation can be compared in these species with different life histories.     

The comparative effects of metals on the hatching of earthworm cocoons

To establish the use of Metaphire posthuma as a sensitive model for ecotoxicological studies, the comparative effects of five metals on the hatching profiles of the cocoons of the earthworms, Metaphire posthuma, Eisenia foetida and Perionyx excavatus, were studied. The cocoons of the three species of earthworms were exposed to copper, chromium (III), chromium (VI), lead and zinc at 1.25, 2.5, 5.0 and 10.0 ppm. Viable cocoons were incubated at 20 +/- degrees C by using the immersion method. The results indicated that the inhibition of cocoon hatching was concentration dependent. The normal hatching, delayed hatching and non-viability of cocoons were recorded. At a concentration of 1.25 ppm, there was almost no effect on the hatching of the cocoons of all three species of earthworms, except when exposed to chromium (VI), but higher concentrations (2.5 and 5.0 ppm) caused severe effects. It was concluded that M. posthuma was more sensitive than the other two species, and that it is a suitable model for use in ecotoxicity testing.     

In vitro tests within the REACH information strategies

Tonnage-based information requirements are specified in the proposal on the regulation on the Registration, Evaluation and Authorisation of Chemicals (REACH) in the European Union. The hazard assessment for toxic endpoints should be performed by using a tiered approach, i.e. as an information strategy (IS), starting with an evaluation of all of the data already available, including animal in vivo and in vitro data, and human evidence and case reports, as well as data from (Quantitative)-Structure Activity Relationships ([Q]SARs) or read-across, before any further testing is suggested. To contribute to the implementation of the REACH system, the Nordic countries launched two projects: 1) a review of currently used testing strategies, including a comparison with the REACH requirements; and 2) the development of detailed ISs for skin and eye irritation/corrosion. The review showed that the ISs and classification criteria for the selected endpoints are inconsistent in many cases. In the classification criteria, human data and in vivo test results are usually the prerequisites. Other types of information, such as data from in vitro studies, can sometimes be used, but usually as supportive evidence only. This differs from the REACH ISs, where QSARs, read-across and in vitro testing are important elements. In the other part of the project, an IS for skin and eye irritation/corrosion was proposed. The strategy was "tested" by using four high production volume (HPV) chemicals: hydrogen peroxide, methyl tertiary-butyl ether (MTBE), trivalent chromium, and diantimony trioxide, but only MTBE and trivalent chromium are dealt with in this paper. The "test" revealed that in vivo data, human case reports and physical-chemical data were available and could be used in the evaluation. Classification could be based on the proposed IS and the existing data in all cases, except for the eye irritation/corrosion of trivalent chromium. Weight-of-evidence analysis appeared to be a useful step in the ISs proposed, and including it in the REACH strategies should be considered. For these chemicals, few in vitro and (Q)SAR data were available--more of these data would be generated, if the relevant guidance and legislation on classification were updated.     

Selection for population‐specific adaptation shaped patterns of variation in the photoperiod pathway genes in Arabidopsis lyrata during post‐glacial colonization

Spatially varying selection can lead to population‐specific adaptation, which is often recognized at the phenotypic level; however, the genetic evidence is weaker in many groups of organisms. In plants, environmental shifts that occur due to colonization of a novel environment may require adaptive changes in the timing of growth and flowering, which are often governed by location‐specific environmental cues such as day length. We studied locally varying selection in 19 flowering time loci in nine populations of the perennial herb Arabidopsis lyrata, which has a wide but patchy distribution in temperate and boreal regions of the northern hemisphere. The populations differ in their recent population demographic and colonization histories and current environmental conditions, especially in the growing season length. We searched for population‐specific molecular signatures of directional selection by comparing a set of candidate flowering time loci with a genomic reference set within each population using multiple approaches and contrasted the patterns of different populations. The candidate loci possessed approximately 20% of the diversity of the reference loci. On average the flowering time loci had more rare alleles (a smaller Tajima's D) and an excess of highly differentiated sites relative to the reference, suggesting positive selection. The strongest signal of selection was detected in photoperiodic pathway loci in the colonizing populations of Northwestern Europe, whereas no evidence of positive selection was detected in the Central European populations. These findings emphasized the population‐specific nature of selection and suggested that photoperiodic adaptation was important during postglacial colonization of the species.     

Natural variation in Arabidopsis lyrata vernalization requirement conferred by a FRIGIDA indel polymorphism

Species share homologous genes to a large extent, but it isnot yet known to what degree the same loci have been targetsfor natural selection in different species. Natural variationin flowering time is determined to a large degree by 2 genes,FLOWERING LOCUS C and FRIGIDA, in Arabidopsis thaliana. Here,we examine whether FRIGIDA has a role in differences in floweringtime between and within natural populations of Arabidopsis lyrata,a close outcrossing perennial relative of A. thaliana. We found2 FRIGIDA sequence variants producing potentially functionalproteins but with a length difference of 14 amino acids. Thesevariants conferred a 15-day difference in flowering time inan association experiment in 2 Scandinavian populations. Thedifference in flowering time between alleles was confirmed withtransformation to A. thaliana. Because the north European late-floweringpopulations harbor both late- and early sequence variants atintermediate frequencies and the late-flowering variant is mostfrequent in the southern early flowering European population,other genetic factors must be responsible for the floweringtime differences between the populations. The length polymorphismoccurs at high frequencies also in several North American populations.The occurrence of functional variants at intermediate frequenciesin several populations suggests that the variation may be maintainedby balancing selection. This is in contrast to A. thaliana,where independent loss-of-function mutations at the FRIGIDAgene are responsible for differences between populations andlocal adaptation.     

Secretion of the Hormoconis resinae glucoamylase P enzyme from Trichoderma reesei directed by the natural and the cbh1 gene secretion signal

Abstract We have isolated two alkaline phosphatases (H-AP and L-AP, for high and low molecular mass, respectively) from Pseudomonas aeruginosa PA01. These two enzymes were found to differ in mobility on sodium dodecyl sulphate polyacrylamide gels (H-AP, M _r = 51 000 and L-AP, M _r = 39 500), amino-terminal amino acid sequence and did not cross-react. Both enzymes were active as phosphomonoesterases while only L-AP demonstrated any phosphodiesterase activity. Both enzymes were purified from P. aeruginosa grown in phosphate limiting conditions using the same protocol and were identified in both periplasmic and extracellular locations. A low level of H-AP was produced constitutively whereas L-AP was produced only after induction by reduced phosphate concentration in the growth medium. An L-AP-like enzyme has been previously described, however, this is the first report of a second P. aeruginosa alkaline phosphatase.     

Genetic basis of adaptation: flowering time in Arabidopsis thaliana

 We have mapped QTLs (quantitative trait loci) for an adaptive trait, flowering time, in a selfing annual, Arabidopsis thaliana. To obtain a mapping population we made a cross between an early-summer, annual strain, Li-5, and an individual from a late over-wintering natural population, Naantali. From the backcross to Li-5 298 progeny were grown, of which 93 of the most extreme individuals were genotyped. The data were analysed with both interval mapping and composite interval mapping methods to reveal one major and six minor QTLs, with at least one QTL on each of the five chromosomes. The QTL on chromosome 4 was a major one with an effect of 17.3 days on flowering time and explaining 53.4% of the total variance. The others had effects of at most 6.5 days, and they accounted for only small portions of the variance. Epistasis was indicated between one pair of the QTLs. The result of finding one major QTL and little epistasis agrees with previous studies on flowering time in Arabidopsis thaliana and other species. That several QTLs were found was expected considering the large number of possible candidate loci. In the light of the suggested genetic models of gene action at the candidate loci, epistasis was to be expected. The data showed that major QTLs for adaptive traits can be detected in non-domesticated species. Received: 15 January 1997/Accepted: 21 February 1997     

Plasma copeptin in the assessment of febrile neutropenia

Copeptin, the surrogate marker of arginine vasopressin (AVP), has been suggested to be a useful biomarker in monitoring sepsis reflecting hemodynamic imbalance and stress state. This prospective study conducted at a hematology ward in a Finnish University Hospital aimed to investigate whether plasma copeptin predicts the development of complicated course of neutropenic fever (bacteremia or need for treatment at intensive care unit) in 100 hematological patients experiencing their first neutropenic fever episode after intensive chemotherapy for hematological malignancy. Contrary to study presumptions, not elevated copeptin but the lack of a proper initial increase of plasma copeptin (<0.02 ng/mL from day 0 to day 1) predicted blood culture positive sepsis (p=0.023) and gram-negative bacteremia (p=0.045). No correlation was observed with plasma sodium, blood pressure or evaluated osmolality. Plasma copeptin correlated inversely with the same day pentraxin 3 on day 0-day 2 (all p-values <0.001) and with C-reactive protein on day 1 (p=0.015). In conclusion, copeptin did not correlate with disease severity, but the lack of a proper initial increase was associated with bacteremic complications of febrile neutropenia in hematological patients. The findings suggest the possibility of central dysregulation of AVP release and do not support the use of copeptin as a biomarker of septic complications in this patient group.     

Comparative gene mapping in Arabidopsis lyrata chromosomes 1 and 2 and the corresponding A. thaliana chromosome 1: recombination rates, rearrangements and centromere location

To add detail to the genetic map of Arabidopsis lyrata, and compare it with that of A. thaliana, we have developed many additional markers in the A. lyrata linkage groups, LG1 and LG2, corresponding to A. thaliana chromosome 1. We used a newly developed method for marker development for single nucleotide polymorphisms present in gene sequences, plus length differences, to map genes in an A. lyrata family, including variants in several genes close to the A. thaliana centromere 1, providing the first data on the location of an A. lyrata centromere; we discuss the implications for the evolution of chromosome 1 of A. thaliana. With our larger marker density, large rearrangements between the two Arabidopsis species are excluded, except for a large inversion on LG2. This was previously known in Capsella; its presence in A. lyrata suggests that, like most other rearrangements, it probably arose in the A. thaliana lineage. Knowing that marker orders are similar, we can now compare homologous, non-rearranged map distances to test the prediction of more frequent crossing-over in the more inbreeding species. Our results support the previous conclusion of similar distances in the two species for A. lyrata LG1 markers. For LG2 markers, the distances were consistently, but non-significantly, larger in A. lyrata. Given the two species' large DNA content difference, the similarity of map lengths, particularly for LG1, suggests that crossing-over is more frequent across comparable physical distances in the inbreeder, A. thaliana, as predicted.