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T Säll

Publications and source records attributed to T Säll.

16 recordsLinked to original sources
PubMed2007

The evolutionary history of the common chloroplast genome of Arabidopsis thaliana and A. suecica.

The evolutionary history of the common chloroplast (cp) genome of the allotetraploid Arabidopsis suecica and its maternal parent A. thaliana was investigated by sequencing 50 fragments of cpDNA, resulting in 98 polymorphic sites. The variation in the A. suecica sample was small, in contrast to that of the A. thaliana sample. The time to the most recent common ancestor (T(MRCA)) of the A. suecica cp genome alone was estimated to be about one 37th of the T(MRCA) of both the A. thaliana and A. suecica cp genomes. This corresponds to A. suecica having a MRCA between 10 000 and 50 000 years ago, suggesting that the entire species originated during, or before, this period of time, although the estimates are sensitive to assumptions made about population size and mutation rate. The data was also consistent with the hypothesis of A. suecica being of single origin. Isolation-by-distance and population structure in A. thaliana depended upon the geographical scale analysed; isolation-by-distance was found to be weak on the global scale but locally pronounced. Within the genealogical cp tree of A. thaliana, there were indications that the root of the A. suecica species is located among accessions of A. thaliana that come primarily from central Europe. Selective neutrality of the cp genome could not be rejected, despite the fact that it contains several completely linked protein-coding genes.

Arabidopsis↗
PubMed2003

Chloroplast DNA indicates a single origin of the allotetraploid Arabidopsis suecica.

DNA sequencing was performed on up to 12 chloroplast DNA regions [giving a total of 4288 base pairs (bp) in length] from the allopolyploid Arabidopsis suecica (48 accessions) and its two parental species, A. thaliana (25 accessions) and A. arenosa (seven accessions). Arabidopsis suecica was identical to A. thaliana at all 93 sites where A. thaliana and A. arenosa differed, thus showing that A. thaliana is the maternal parent of A. suecica. Under the assumption that A. thaliana and A. arenosa separated 5 million years ago, we estimated a substitution rate of 2.9 x 10(-9) per site per year in noncoding single copy sequence. Within A. thaliana we found 12 substitution (single bp) and eight insertion/deletion (indel) polymorphisms, separating the 25 accessions into 15 haplotypes. Eight of the A. thaliana accessions from central Sweden formed one cluster, which was separated from a cluster consisting of central European and extreme southern Swedish accessions. This latter cluster also included the A. suecica accessions, which were all identical except for one 5 bp indel. We interpret this low level of variation as a strong indication that A. suecica effectively has a single origin, which we dated at 20 000 years ago or more.

Arabidopsis↗
PubMed2002

Genetic variation in Arabidopsis suecica and its parental species A. arenosa and A. thaliana.

Random amplified polymorphic DNA (RAPD) markers were used to estimate the level of genetic variation in Swedish accessions of the allopolyploid Arabidopsis suecica and its parental species A. thaliana and A. arenosa. The results showed clear differences among the three species with respect to the level of variation. A. arenosa was highly variable, A. thaliana showed a moderate level of variation whereas A. suecica was much less variable than the two other species. An extended analysis covering 19 Swedish populations of A. suecica corroborated the low level of variation in this species, yet 16 unique phenotypes were observed. No isolation by distance was observed. When the genetic variation was partitioned among and within populations of A. suecica, the results showed that the majority of the variation (81%) occurred among populations. This result is interpreted as a strong indication that A. suecica is autogamous in nature.

Arabidopsis↗
PubMed2001

Identification of cytogenetic subgroups and karyotypic pathways in transitional cell carcinoma.

The clinical course in urinary bladder cancer is difficult or impossible to predict based on conventional disease parameters. It is a reasonable hypothesis that the genetic aberrations acquired by the tumor cells, being instrumental in bringing about the disease in the first place, may also hold the key to more reliable prognostication. However, though 200 transitional cell carcinomas (TCC), the most common bladder cancer in the Western world, with clonal chromosomal abnormalities have been reported, our knowledge about the karyotypic characteristics of these tumors remains insufficient. The aberration pattern is clearly nonrandom, but no completely specific primary or secondary karyotypic abnormality has been identified, and the chronological order in which the aberrations appear during disease progression is not well known. The high degree of karyotypic complexity in epithelial tumors like TCC is one reason why our picture of the sequential order of cytogenetic evolution is unclear. To overcome some of these difficulties we have used several statistical methods that allow analysis and interpretation of the relationship between cytogenetic aberrations in TCC. We show that there exists a temporal order with respect to the appearance of chromosomal imbalances and that this order is highly correlated with tumor stage and grade. Analyzing changes in the distribution of imbalances per tumor in G1, G2, and G3 tumors, we suggest that progression involves the acquisition of cytogenetically detectable and submicroscopic genetic changes at comparable frequencies. By means of computer simulations, we show that the imbalances -9, +7, and 1q+ appear earlier than expected from random events and that -6q, -5q, -18, +5p, -22p, and -15 appear later than expected. Using principal component analysis, we identify two cytogenetic pathways in TCC, one initiated by -9 and followed by -11p and 1q+, the other initiated by +7 and followed by 8p- and +8q. The -9 pathway was correlated with stage Ta-T2 tumors, whereas the +7 pathway was correlated with stage T1-T3 tumors, i.e., +7 tumors appeared to be more aggressive. Although these pathways are well separated at earlier stages, they later converge to contain a common set of imbalances.

Carcinoma, Transitional Cell↗
PubMed2001

The incidence of trisomy 8 as a sole chromosomal aberration in myeloid malignancies varies in relation to gender, age, prior iatrogenic genotoxic exposure, and morphology.

Although trisomy 8 as a sole change is one of the most common chromosomal abnormalities in myeloid malignancies, it is largely unknown if the incidence of this aberration is influenced by other factors of clinical importance. In the present study, the frequencies of isolated +8 in relation to gender, age, previous treatment with chemo- or radiotherapy, and morphologic subtype were ascertained in published, as well as in our own unpublished, cases of acute myeloid leukemia (AML; n=4,246), myelodysplastic syndromes (MDS; n=1,817), and chronic myeloproliferative disorders (MPD; n=530). The frequencies of +8 were higher in MDS and MPD than in AML (7.5% vs. 5.6%; P<0.01) and varied among the morphologic subtypes of AML and MDS (P<0.001 and P<0.05, respectively). Trisomy 8 was more common in women than in men with MPD (11% vs. 5.1%; P<0.05). Furthermore, the frequencies of +8 were higher in de novo AML and MDS than in treatment-related cases (6.0% vs. 2.8%; P<0.01 and 8.6% vs. 1.5%; P<0.001, respectively). The incidence also varied significantly with age in AML (P<0.001), being more common in elderly patients. Although the causes for this frequency heterogeneity remain to be elucidated, possible explanations may include different environmental exposures affecting the origin of +8 in AML, MDS, and MPD and the presence of different underlying cryptic primary aberrations.

Age Factors↗
PubMed2001

Multivariate analyses of genomic imbalances in solid tumors reveal distinct and converging pathways of karyotypic evolution.

A total of 3,016 malignant solid tumors (kidney, colorectal, breast, head and neck, ovarian, and lung carcinomas, neuroglial tumors, malignant melanoma, and testicular germ cell tumors) were selected for statistical analyses regarding karyotypic evolution. Genomic imbalances, i.e., net gains and losses, present in more than 5% of each tumor type were identified. Individual tumors were then classified with respect to absence or presence of these imbalances. To analyze for possible patterns of correlated imbalances, principal component analyses (PCA) were performed. Furthermore, algorithms were developed to analyze the temporal order of the imbalances, as well as the possible selection for early or late appearance in the karyotypic evolution. By analyzing the temporal order of imbalances common to many tumor types, a general order for nine of these emerged, namely, +7, -3p, -6q, -1p, -8p, -17p, -9p, -18, and -22. The distributions of the number of imbalances per case revealed a geometrical distribution, ranging from one to nine imbalances per tumor, in the majority of the tumor types. In tumor types in which cases with a high number of imbalances per case were frequent, notably head and neck, ovarian, and lung carcinomas, the overall distributions were bimodal, indicating the presence of two modes of chromosome evolution. By combining data from the PCA with the temporal analyses, it was possible to identify karyotypic pathways. It was found that the majority of the tumor types displayed more than one cytogenetic route, but, as the karyotypic evolution continued, these converged to a common pathway.

Allelic Imbalance↗
PubMed2001

Linkage disequilibrium mapping of the bolting gene in sea beet using AFLP markers.

The possibility of using linkage disequilibrium mapping in natural plant populations was assessed. In studying linkage disequilibrium among 137 mapped AFLP markers in four populations of sea beet (Beta vulgaris ssp. maritima (L.) Arcang.) it was shown that tightly linked loci could be detected by screening for associations. It was hypothesized that the short distances spanned by linkage disequilibrium enable markers that are very tightly linked to a target gene to be identified. The hypothesis was tested by whole-genome screening of AFLP markers for association with the gene for the annual growth habit, the B gene, in a sample of 106 sea beets. Despite the dominant nature of AFLP, two markers showing significant linkage disequilibrium with the B gene were detected. The results indicate the potential use of linkage disequilibrium for gene mapping in natural plant populations.

Alleles↗
PubMed2000

Primer mixtures in RAPD analysis.

RAPD (random amplified polymorphic DNA) is a multiplex marker system that conventionally uses single-primer PCR to amplify random DNA fragments. Because of its multiplex nature, it is frequently used in bulked segregant analysis (BSA). In view of the very large numbers of markers BSA often requires, we investigated the use of mixtures of primers as a method of increasing the number of markers available. Theoretically, if a single-primer reaction produces x bands on average, an unrestrained PCR process using a primers should produce xa2 bands. Initially, we investigated mixtures containing from one to five primers. The average number of products increased slightly from the single-primer to the multiple-primer case, whereas it was rather constant for the different multi-primer combinations. This deviation from the theoretical expectations, which we attribute to the effects of competition, shows mixtures of more than two primers to be inefficient. The properties of two-primer mixtures in which the proportions of the two primers were varied were also investigated. The intensities of most of the products were influenced by the proportions of the primers used to create the mixture. A good fit was obtained to a model in which the average competitive ability of a band is directly proportional to the probability of randomly obtaining the band-producing primer combination from the pool of primers. Using two-primer mixtures, a(a-1)/2 different two-primer mixtures can be produced. A comparison of different schemes for constructing the two-primer mixtures indicates that the degree of resampling is similar for all schemes. In conclusion, the use of two-primer mixtures is a simple but very powerful strategy in BSA as it can generate an extremely large number of markers.

DNA Primers↗
PubMed1999

An evaluation of the use of pooled samples in studies of genetic variation.

When using molecular markers to study genetic variation, either the sampled individuals can be analysed individually or the individuals can be pooled and only the pools analysed (pooled samples). A theoretical investigation was carried out into the use of pooled samples in the detection of alleles and providing maximum likelihood estimates of allele frequency. The results show that, in many cases, pooled samples are more efficient than samples of individuals. Of the different pool sizes studied, small pools containing two or three individuals showed the smallest expected squared error of allele frequency estimates.

Alleles↗
PubMed1998

Positive correlation between recombination rates and levels of genetic variation in natural populations of sea beet (Beta vulgaris subsp. maritima).

The relation between the level of genetic variation and the rate of recombination per physical unit was investigated in sea beet (Beta vulgaris subsp. maritima). The rate of recombination per physical unit was estimated indirectly through marker density in an RFLP linkage map of sugar beet. From this map, we also selected RFLP markers covering two of the nine chromosomes in Beta. The markers were used to estimate the level of genetic variation in three populations of sea beet, two from Italy and one from England. Two estimates of genetic variation were employed, one based on the number of alleles in the sample and the other on heterozygosity. A statistically significant positive correlation was found between recombination rate and genetic variation. Several theoretical explanations for this are discussed, background selection being one. A correlation similar to this has been observed previously in Drosophila, one that was higher than what we obtained for Beta. This is consistent with various biological differences between the two species.

Chenopodiaceae↗
PubMed1995

A model of chiasma reduction of closely formed crossovers.

A model of chiasma reduction is developed, evaluated by computer simulation and discussed in relation to the evolution of interference. The model assumes that adjacently formed crossovers can interact, if there is incomplete sister chromatid cohesion between them, and give rise to a reduced number of chiasmata. In the absence of crossover position interference this leads to a considerable risk of non-disjunction for an average sized chromosome. It is suggested that an important function of crossover interference is to reduce this effect. The question is raised whether chiasma reduction takes place today. Some available cytological data can be interpreted as showing that chiasma reduction occurs in normal meiosis. The possibility of chiasma reduction therefore needs further attention.

Animals↗
PubMed1994

The robustness of recombination frequency estimates in intercrosses with dominant markers.

The robustness of the maximum likelihood estimates of recombination frequencies has been investigated in double intercrosses with complete dominance at both loci. The robustness was investigated with respect to bias in the recombination frequency estimates due to: (1) limited sample sizes, (2) heterogeneity in recombination frequencies between sexes or among meioses and (3) factors that distort the segregation-misclassification or differential viability. In the coupling phase, the recombination frequency estimates are quite robust with respect to most of the investigated factors. Potentially, the most serious cause of a bias is misclassifications, which tend to increase the recombination frequency estimates. In the repulsion phase, misclassifications are particularly serious, leading to extreme discrepancies between true and observed values. In addition, limited sample size and sex differences in recombination can also bias recombination frequency estimates in repulsion. These effects may pose serious problem in genetic mapping with random amplified polymorphic DNA (RAPD) markers.

Animals↗
PubMed1993

Chiasma and recombination data in plants: are they compatible?

It has long been considered that the number of chiasmata formed during meiosis corresponds to the number of crossovers indicated by the genetic map. However, recent investigations in plants show an unexpected discrepancy in the results obtained when calculating the total number of crossover events per meiosis by these two methods. Is this discrepancy due to methodological difficulties? Or is there something fundamentally wrong with our understanding of crossovers and chiasmata?

Crossing Over, Genetic↗
PubMed1990

Cytoplasmic male sterility in beta is associated with structural rearrangements of the mitochondrial DNA and is not due to interspecific organelle transfer.

Chloroplast (ct) and mitochondrial (mt) DNAs from four cytoplasmic male sterile (cms) and 22 normal fertile sugar beet lines and accessions of wild beets from the genus Beta have been compared with restriction analyses and Southern hybridizations. We have used restriction analyses of ctDNA as a phylogenetic marker to confirm the taxonomic relationships between the different cytoplasms. According to the ctDNA data, all four cms cytoplasms belong to the same taxonomic section, Beta. Restriction patterns of ct and mtDNA from fertile accessions produced analogous trees of similarity and showed a close correlation between the organellar DNA diversity and the accepted taxonomic classification of the species studied. However, the mt-DNA restriction profiles of the four cms types differed dramatically from each other and from those of all fertile accessions from the genus. No indication of cytoplasmic introgression was found in any of the four investigated cms types. Southern hybridization to mtDNA revealed variant genomic arrangements in the different fertile and cms cytoplasms, indicating that rearrangement of the mitochondrial genome is a common denominator to the different cms systems in Beta. It may, indeed, be a common property to spontaneously occurring cms in all or most species.

Chloroplasts↗
PubMed1989

Apparent negative interference due to variation in recombination frequencies.

Variation in recombination frequencies may lead to a bias in the estimated interference value in a linkage experiment. Depending on the pattern of variation, the bias may be toward negative interference or toward positive interference, even when there is positive interference at the cytological level. In this paper we have mainly concentrated on the case of negative interference. We use models to quantify this effect when data are derived from a backcross experiment or from the selfing of F1 individuals. The effect is quantitatively similar in the two cases. There is an upper limit to the size the bias may reach for every given level of recombination. Two reported cases of negative interference in Drosophila and cultivated barley fall within this possible parameter range, i.e., the observed negative interference values could--at least in principle--be due solely to a variation in the recombination frequencies in the experiments.

Analysis of Variance↗