A variant of the tandem duplication - random loss model of genome rearrangement

In Soda'06, Chaudhuri, Chen, Mihaescu and Rao study algorithmic properties of the tandem duplication - random loss model of genome rearrangement, well-known in evolutionary biology. In their model, the cost of one step of duplication-loss of width k is $\alpha^k$ for $\alpha =1$ or $\alpha >=2$. In this paper, we study a variant of this model, where the cost of one step of width $k$ is 1 if $k K$, for any value of the parameter $K in N$. We first show that permutations obtained after $p$ steps of width $K$ define classes of pattern-avoiding permutations. We also compute the numbers of duplication-loss steps of width $K$ necessary and sufficient to obtain any permutation of $S_n$, in the worst case and on average. In this second part, we may also consider the case $K=K(n)$, a function of the size $n$ of the permutation on which the duplication-loss operations are performed

Sex-Specific Crossover Distributions and Variations in Interference Level along Arabidopsis thaliana Chromosome 4

In many species, sex-related differences in crossover (CO) rates have been described at chromosomal and regional levels. In this study, we determined the CO distribution along the entire Arabidopsis thaliana Chromosome 4 (18 Mb) in male and female meiosis, using high density genetic maps built on large backcross populations (44 markers, >1,300 plants). We observed dramatic differences between male and female map lengths that were calculated as 88 cM and 52 cM, respectively. This difference is remarkably parallel to that between the total synaptonemal complex lengths measured in male and female meiocytes by immunolabeling of ZYP1 (a component of the synaptonemal complex). Moreover, CO landscapes were clearly different: in particular, at both ends of the map, male CO rates were higher (up to 4-fold the mean value), whereas female CO rates were equal or even below the chromosomal average. This unique material gave us the opportunity to perform a detailed analysis of CO interference on Chromosome 4 in male and female meiosis. The number of COs per chromosome and the distances between them clearly departs from randomness. Strikingly, the interference level (measured by coincidence) varied significantly along the chromosome in male meiosis and was correlated to the physical distance between COs. The significance of this finding on the relevance of current CO interference models is discussed

SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping

<p>Abstract</p> <p>Background</p> <p>With the increasing availability of EST databases and whole genome sequences, SNPs have become the most abundant and powerful polymorphic markers. However, SNP chip data generally suffers from ascertainment biases caused by the SNP discovery and selection process in which a small number of individuals are used as discovery panels. The ongoing International Citrus Genome Consortium sequencing project of the highly heterozygous Clementine and sweet orange genomes will soon result in the release of several hundred thousand SNPs. The primary goals of this study were: (i) to estimate the transferability within the genus <it>Citrus </it>of SNPs discovered from Clementine BACend sequencing (BES), (ii) to estimate bias associated with the very narrow discovery panel, and (iii) to evaluate the usefulness of the Clementine-derived SNP markers for diversity analysis and comparative mapping studies between the different cultivated <it>Citrus </it>species.</p> <p>Results</p> <p>Fifty-four accessions covering the main <it>Citrus </it>species and 52 interspecific hybrids between pummelo and Clementine were genotyped on a GoldenGate array platform using 1,457 SNPs mined from Clementine BES and 37 SNPs identified between and within <it>C. maxima, C. medica, C. reticulata </it>and <it>C. micrantha</it>. Consistent results were obtained from 622 SNP loci. Of these markers, 116 displayed incomplete transferability primarily in <it>C. medica, C. maxima </it>and wild <it>Citrus </it>species. The two primary biases associated with the SNP mining in Clementine were an overestimation of the <it>C. reticulata </it>diversity and an underestimation of the interspecific differentiation. However, the genetic stratification of the gene pool was high, with very frequent significant linkage disequilibrium. Furthermore, the shared intraspecific polymorphism and accession heterozygosity were generally enough to perform interspecific comparative genetic mapping.</p> <p>Conclusions</p> <p>A set of 622 SNP markers providing consistent results was selected. Of the markers mined from Clementine, 80.5% were successfully transferred to the whole <it>Citrus </it>gene pool. Despite the ascertainment biases in relation to the Clementine origin, the SNP data confirm the important stratification of the gene pools around <it>C. maxima, C. medica </it>and <it>C. reticulata </it>as well as previous hypothesis on the origin of secondary species. The implemented SNP marker set will be very useful for comparative genetic mapping in <it>Citrus </it>and genetic association in <it>C. reticulata</it>.</p

Discovery and mapping of a new expressed sequence tag-single nucleotide polymorphism and simple sequence repeat panel for large-scale genetic studies and breeding of Theobroma cacao L.

Theobroma cacao is an economically important tree of several tropical countries. Its genetic improvement is essential to provide protection against major diseases and improve chocolate quality. We discovered and mapped new expressed sequence tag-single nucleotide polymorphism (EST-SNP) and simple sequence repeat (SSR) markers and constructed a high-density genetic map. By screening 149 650 ESTs, 5246 SNPs were detected in silico, of which 1536 corresponded to genes with a putative function, while 851 had a clear polymorphic pattern across a collection of genetic resources. In addition, 409 new SSR markers were detected on the Criollo genome. Lastly, 681 new EST-SNPs and 163 new SSRs were added to the pre-existing 418 co-dominant markers to construct a large consensus genetic map. This high-density map and the set of new genetic markers identified in this study are a milestone in cocoa genomics and for marker-assisted breeding. The data are available at http://tropgenedb.cirad.fr

Risk of lung cancer mortality in nuclear workers from internal exposure to alpha particle-emitting radionuclides

BACKGROUND: Carcinogenic risks of internal exposures to alpha-emitters (except radon) are poorly understood. Since exposure to alpha particles-particularly through inhalation-occurs in a range of settings, understanding consequent risks is a public health priority. We aimed to quantify dose-response relationships between lung dose from alpha-emitters and lung cancer in nuclear workers. METHODS: We conducted a case-control study, nested within Belgian, French, and UK cohorts of uranium and plutonium workers. Cases were workers who died from lung cancer; one to three controls were matched to each. Lung doses from alpha-emitters were assessed using bioassay data. We estimated excess odds ratio (OR) of lung cancer per gray (Gy) of lung dose. RESULTS: The study comprised 553 cases and 1,333 controls. Median positive total alpha lung dose was 2.42 mGy (mean: 8.13 mGy; maximum: 316 mGy); for plutonium the median was 1.27 mGy and for uranium 2.17 mGy. Excess OR/Gy (90% confidence interval)-adjusted for external radiation, socioeconomic status, and smoking-was 11 (2.6, 24) for total alpha dose, 50 (17, 106) for plutonium, and 5.3 (-1.9, 18) for uranium. CONCLUSIONS: We found strong evidence for associations between low doses from alpha-emitters and lung cancer risk. The excess OR/Gy was greater for plutonium than uranium, though confidence intervals overlap. Risk estimates were similar to those estimated previously in plutonium workers, and in uranium miners exposed to radon and its progeny. Expressed as risk/equivalent dose in sieverts (Sv), our estimates are somewhat larger than but consistent with those for atomic bomb survivors.See video abstract at, http://links.lww.com/EDE/B232

2es Rencontres FORMIST - 2002 (Actes complets)

Actes des 2èmes Rencontres FORMIST : Le point sur la formation des usagers ; Réseaux.Doc : formation à la recherche documentaire ; Les formations à l\u27information ; Séduction et partenariat : mise en œuvre de la formation des usagers aux bibliothèques de l\u27Université Libre de Bruxelles ; Formation des étudiants à la maîtrise de l\u27information ; l\u27expérience de l\u27Université des Sciences sociales de Toulouse 1 ; Méthodologie documentaire en BU Sciences : l\u27exemple de Nice, témoignage d\u27une expérience de terrain ; Formation à la recherche documentaire au sein de la Faculté de pharmacie de Lyon (Université Claude-Bernard Lyon 1) ; Un module de méthodologie du travail universitaire original : STIM-Sciences de la Terre en images ; Pédagogie classique versus pédagogie par projets et pédagogie inverse : l\u27expérience de l\u27INSA de Lyon ; La méthodologie du travail universitaire à la bibliothèque de Droit et de Lettres de l\u27Université de La Réunion ; Tables-rondes et synthèse