Distribution dynamics of the Tnt1 retrotransposon in tobacco

Retrotransposons contribute significantly to the size, organization and genetic diversity of plant genomes. Although many retrotransposon families have been reported in plants, to this day, the tobacco Tnt1 retrotransposon remains one of the few elements for which active transposition has been shown. Demonstration that Tnt1 activation can be induced by stress has lent support to the hypothesis that, under adverse conditions, transposition can be an important source of genetic variability. Here, we compared the insertion site preference of a collection of newly transposed and pre-existing Tnt1 copies identified in plants regenerated from protoplasts or tissue culture. We find that newly transposed Tnt1 copies are targeted within or close to host gene coding sequences and that the distribution of pre-existing insertions does not vary significantly from this trend. Therefore, in spite of their potential to disrupt neighboring genes, insertions within or near CDS are not preferentially removed with age. Elimination of Tnt1 insertions within or near coding sequences may be relaxed due to the polyploid nature of the tobacco genome. Tnt1 insertions within or near CDS are thus better tolerated and can putatively contribute to the diversification of tobacco gene function. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Retroelements in higher plants.

Representatives of several classes of retroelements have been characterized in a broad range of plant species, where they appear at variable and sometimes very high copy numbers. So far, only a very small number of plant elements have been shown to be active, and this activity seems to be restricted to specific situations of 'genomic shock'. Although it is not yet known whether the presence of retroelements is linked to the high level of variability found in plant genomes, it is now clear that retrotransposons are ancient and ubiquitous components of plant genomes, and could play an important role in plant evolution.     

Maize genetic diversity and association mapping using transposable element insertion polymorphisms

Transposable elements are the major component of the maize genome and presumably highly polymorphic yet they have not been used in population genetics and association analyses. Using the Transposon Display method, we isolated and converted into PCR-based markers 33 Miniature Inverted Repeat Transposable Elements (MITE) polymorphic insertions. These polymorphisms were genotyped on a population-based sample of 26 American landraces for a total of 322 plants. Genetic diversity was high and partitioned within and among landraces. The genetic groups identified using Bayesian clustering were in agreement with published data based on SNPs and SSRs, indicating that MITE polymorphisms reflect maize genetic history. To explore the contribution of MITEs to phenotypic variation, we undertook an association mapping approach in a panel of 367 maize lines phenotyped for 26 traits. We found a highly significant association between the marker ZmV1-9, on chromosome 1, and male flowering time. The variance explained by this association is consistent with a flowering delay of +123 degree-days. This MITE insertion is located at only 289 nucleotides from the 3′ end of a Cytochrome P450-like gene, a region that was never identified in previous association mapping or QTL surveys. Interestingly, we found (i) a non-synonymous mutation located in the exon 2 of the gene in strong linkage disequilibrium with the MITE polymorphism, and (ii) a perfect sequence homology between the MITE sequence and a maize siRNA that could therefore potentially interfere with the expression of the Cytochrome P450-like gene. Those two observations among others offer exciting perspectives to validate functionally the role of this region on phenotypic variation.     

RNA-mediated transposition of the tobacco retrotransposon Tnt1 in Arabidopsis thaliana.

The tobacco (Nicotiana tabacum) retrotransposon Tnt1 was introduced into Arabidopsis thaliana. In this heterologous host plant species, Tnt1 undergoes an RNA-mediated transposition and creates a 5 bp duplication at the insertion sites. This is the first report of transposition of a retrotransposon after introduction into a heterologous host species. Tnt1 transposed during in vitro regeneration of transformed A.thaliana, but no transposition event was detected as happening in T2 and T3 generation plants. Newly synthesized copies of Tnt1 can integrate into coding regions of the host DNA. Our results open up the possibility of using Tnt1 as a new tool for insertional mutagenesis and functional analysis of plant genomes, in addition to the strategies of T-DNA and transposon tagging.     

Daily estimation of the severity of multiple organ dysfunction syndrome in critically ill children

Background

Daily evaluation of multiple organ dysfunction syndrome has been performed in critically ill adults. We evaluated the clinical course of multiple organ dysfunction over time in critically ill children using the Pediatric Logistic Organ Dysfunction (PELOD) score and determined the optimal days for measuring scores.

Methods

We prospectively measured daily PELOD scores and calculated the change in scores over time for 1806 consecutive patients admitted to seven pediatric intensive care units (PICUs) between September 1998 and February 2000. To study the relationship between daily scores and mortality in the PICU, we evaluated changes in daily scores during the first four days; the mean rate of change in scores during the entire PICU stay between survivors and nonsurvivors; and Cox survival analyses using a change in PELOD score as a time-dependent covariate to determine the optimal days for measuring daily scores.

Results

The overall mortality among the 1806 patients was 6.4%. A high PELOD score (≥ 20 points) on day 1 was associated with an odds ratio (OR) for death of 40.7 (95% confidence interval [CI] 20.3–81.4); a medium score (10–19 points) on day 1 was associated with an OR for death of 4.2 (95% CI 2.0–8.7). Mortality was 50% when a high score on day 1 increased on day 2. The course of daily PELOD scores differed between survivors and nonsurvivors. A set of seven days (days 1, 2, 5, 8, 12, 16 and 18) was identified as the optimal period for measurement of daily PELOD scores.

Interpretation

PELOD scores indicating a worsening condition or no improvement over time were indicators of a poor prognosis in the PICU. A set of seven days for measurement of the PELOD score during the PICU stay provided optimal information on the progression of multiple-organ dysfunction syndrome in critically ill children.Almost all patients in intensive care units (ICUs) have some organ dysfunction.^1–4 Adult and pediatric studies have shown that mortality increases with the number of organs involved.^2,4,5 Thus, multiple-organ dysfunction syndrome (dysfunction involving two or more organs) has been viewed as the inexorable pathway to death.⁶ Primary multiple-organ dysfunction syndrome (present at admission or occurring within the first week after admission to the ICU) accounts for 88% of children with the syndrome; secondary multiple-organ dysfunction syndrome is less common (12%) but is associated with higher morbidity and mortality.⁷Organ dysfunction scores were first developed for use in critically ill adults to describe and quantify the severity of organ dysfunction, not to predict mortality. Two scores have been proposed for critically ill children: the Pediatric Logistic Organ Dysfunction (PELOD) score and the Pediatric Multiple Organ Dysfunction Score (P-MODS).^8–10 These scores quantify organ dysfunction precisely and can be used as indicators of the severity of illness throughout the clinical course. They can also be used as baseline and outcome measures in clinical studies conducted in ICUs^11,12 and pediatric ICUs (PICUs).¹³The PELOD score calculated with data collected over the entire PICU stay has been validated (using the most abnormal value of each variable during the entire PICU stay).¹⁰ However, the PELOD score over the entire PICU stay cannot be calculated before discharge from the unit; therefore, it cannot be used to characterize and follow the severity of organ dysfunction on a daily basis. Measurements repeated daily may provide more useful information.¹⁴ The optimal period for measuring daily scores for multiple organ dysfunction in adults has been studied.^15–17 Indeed, trends in the Sequential Organ Failure Assessment score over the first 48 hours in the ICU was found to be a sensitive indicator of outcome, with decreasing scores associated with a decrease in mortality from 50% to 27%.¹⁷ Similar data for critically ill children are lacking.We conducted this study to describe the clinical course of multiple organ dysfunction over time as measured by the daily PELOD score. Because the time and effort necessary to ensure accurate daily assessments and data entry can be substantial,¹⁸ we also aimed to determine the optimal days for measuring daily scores during the PICU stay.