Biomedical subjects

C Vitte

Publications and source records attributed to C Vitte.

6 recordsLinked to original sources

PubMed2005

LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model.

Long Terminal Repeat (LTR) retrotransposons are ubiquitous components of plant genomes. Because of their copy-and-paste mode of transposition, these elements tend to increase their copy number while they are active. In addition, it is now well established that the differences in genome size observed in the plant kingdom are accompanied by variations in LTR retrotransposon content, suggesting that LTR retrotransposons might be important players in the evolution of plant genome size, along with polyploidy. The recent availability of large genomic sequences for many crop species has made it possible to examine in detail how LTR retrotransposons actually drive genomic changes in plants. In the present paper, we provide a review of the recent publications that have contributed to the knowledge of plant LTR retrotransposons, as structural components of the genomes, as well as from an evolutionary genomic perspective. These studies have shown that plant genomes undergo genome size increases through bursts of retrotransposition, while there is a counteracting process that tends to eliminate the transposed copies from the genomes. This process involves recombination mechanisms that occur either between the LTRs of the elements, leading to the formation of solo-LTRs, or between direct repeats anywhere in the sequence of the element, leading to internal deletions. All these studies have led to the emergence of a new model for plant genome evolution that takes into account both genome size increases (through retrotransposition) and decreases (through solo-LTR and deletion formation). In the conclusion, we discuss this new model and present the future prospects in the study of plant genome evolution in relation to the activity of transposable elements.

Flowers↗

PubMed2004

Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.).

The origin of rice domestication has been the subject of debate for several decades. We have compared the transpositional history of 110 LTR retrotransposons in the genomes of two rice varieties, Nipponbare (Japonica type) and 93-11 (Indica type) whose complete sequences have recently been released. Using a genomic paleontology approach, we estimate that these two genomes diverged from one another at least 200,000 years ago, i.e., at a time which is clearly older than the date of domestication of the crop (10,000 years ago, during the late Neolithic). In addition, we complement and confirm this first in silico analysis with a survey of insertion polymorphisms in a wide range of traditional rice varieties of both Indica and Japonica types. These experimental data provide additional evidence for the proposal that Indica and Japonica rice arose from two independent domestication events in Asia.

Base Sequence↗

PubMed2003

Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L.

We studied the dynamics of hopi, Retrosat1, and RIRE3, three gypsy-like long terminal repeat (LTR) retrotransposons, in Oryza sativa L. genome. For each family, we assessed the phenetic relationships of the copies and estimated the date of insertion of the complete copies through the evaluation of their LTR divergence. We show that within each family, distinct phenetic groups have inserted at significantly different times, within the past 5 Myr and that two major amplification events may have occurred during this period. We show that solo-LTR formation through homologous unequal recombination has occurred in rice within the past 5 Myr for the three elements. We thus propose an increase/decrease model for rice genome evolution, in which both amplification and recombination processes drive variations in genome size.

Animals↗

PubMed2002

Characterization of transposable elements in the genome of rice (Oryza sativa L.) using Representational Difference Analysis (RDA).

Representational Difference Analysis was applied to characterize genomic differentiations between rice ( Oryza sativa) and foxtail millet ( Setaria italica) and subsequently to identify rice transposable elements. Rice was used as the tester and millet as the driver. A total of eleven, non-redundant, positive clones were isolated from the library. Their analysis revealed that they all represent dispersed repetitive DNA sequences. In addition, homology searches using the BLAST procedure showed that they correspond to seven distinct rice transposable elements. Three had been previously identified as gypsy-like retroelements ( Retrosat1, RIRE3 and RIRE8). The remaining four are novel: we named them hipa (a CACTA-like transposon), houba (a copia-like retroelement), hopi and dagul (two gypsy-like retroelements). The RDA clones were used as probes in Southern hybridization experiments with genomic DNAs of several species from the family Poaceae. The results suggest that the genomic differentiations associated with the activity of these transposable elements are of relatively recent origin. In addition, comparison of the hybridization patterns obtained for several Oryza species suggests that several independent amplifications of these transposable elements might have occurred within the genus.

Base Sequence↗

PubMed2001

DNA diversity in sex-linked and autosomal genes of the plant species Silene latifolia and Silene dioica.

The relatively recent origin of sex chromosomes in the plant genus Silene provides an opportunity to study the early stages of sex chromosome evolution and, potentially, to test between the different population genetic processes likely to operate in nonrecombining chromosomes such as Y chromosomes. We previously reported much lower nucleotide polymorphism in a Y-linked gene (SlY1) of the plant Silene latifolia than in the homologous X-linked gene (SlX1). Here, we report a more extensive study of nucleotide diversity in these sex-linked genes, including a larger S. latifolia sample and a sample from the closely related species Silene dioica, and we also study the diversity of an autosomal gene, CCLS37.1. We demonstrate that nucleotide diversity in the Y-linked genes of both S. latifolia and S. dioica is very low compared with that of the X-linked gene. However, the autosomal gene also has low DNA polymorphism, which may be due to a selective sweep. We use a single individual of the related hermaphrodite species Silene conica, as an outgroup to show that the low SlY1 diversity is not due to a lower mutation rate than that for the X-linked gene. We also investigate several other possibilities for the low SlY1 diversity, including differential gene flow between the two species for Y-linked, X-linked, and autosomal genes. The frequency spectrum of nucleotide polymorphism on the Y chromosome deviates significantly from that expected under a selective-sweep model. However, we detect population subdivision in both S. latifolia and S. dioica, so it is not simple to test for selective sweeps. We also discuss the possibility that Y-linked diversity is reduced due to highly variable male reproductive success, and we conclude that this explanation is unlikely.

DNA, Plant↗

PubMed1995

Osteoblast adherence and resorption activity of isolated osteoclasts on calcium sulphate hemihydrate.

The adherence of osteoblast-like cells and the resorption activity of isolated osteoclasts on calcium sulphate hemihydrate (CSH) was investigated. After a 24 h incubation period, alkaline phosphatase staining showed that rat osteoblast-like cells ROS 17/2.8 attached on CSH. Neutral red (NR) and tartrate-resistant acid phosphatase (TRAP) staining revealed that osteoclasts attached on CSH. Furthermore, osteoclasts formed lacunae as revealed by scanning electron microscopy. Although the lacunae formed by osteoclasts on CSH were diverse in shape and form, the most common type had approximately a circular outline, with a well-defined margin similar to those formed on dentine. Less commonly, excavations appeared as a discontinuous area of resorbed CSH with the presence of a circular zone around the non-resorbed area. Finally, by using 10(-9) M calcitonin, evidence was obtained that NR-positive cells were osteoclasts (58.3% and 57.66% decrease of NR-positive mouse and rat cells detected on CSH after 24 h incubation). However, no inhibition was obtained with 10(-11) M calcitonin. The overall number of NR-positive osteoclasts adherent on 256 mm2 CSH was 43 +/- 14 and 42 +/- 3 for mice and rat, respectively. The overall number of TRAP-positive mouse osteoclasts was 67 +/- 12. Acetazolamide (10(-5) M), a carbonic anhydrase inhibitor, inhibited the number of adherent NR osteoclasts on CSH by 50.42% and 41.6% for mouse and rat, respectively. These results indicate that osteoblasts attach on CSH and osteoclasts resorb CSH in vitro.

Acetazolamide↗