Contribution of radiation hybrids to genome mapping in domestic animals.

Radiation hybrid mapping has emerged in the end of the 1990 s as a successful and complementary approach to map genomes, essentially because of its ability to bridge the gaps between genetic and clone-based physical maps, but also using comparative mapping approaches, between 'gene-rich' and 'gene-poor' maps. Since its early development in human, radiation hybrid mapping played a pivotal role in the process of mapping animal genomes, especially mammalian ones. We review here all the different steps involved in radiation hybrid mapping from the constitution of panels to the construction of maps. A description of its contribution to whole genome maps with a special emphasis on domestic animals will also be presented. Finally, current applications of radiation hybrid mapping in the context of whole genome assemblies will be described.

A comparative genome approach to marker ordering.

MOTIVATION: Genome maps are fundamental to the study of an organism and essential in the process of genome sequencing which in turn provides the ultimate map of the genome. The increased number of genomes being sequenced offers new opportunities for the mapping of closely related organisms. We propose here an algorithmic formalization of a genome comparison approach to marker ordering. RESULTS: In order to integrate a comparative mapping approach in the algorithmic process of map construction and selection, we propose to extend the usual statistical model describing the experimental data, here radiation hybrids (RH) data, in a statistical framework that models additionally the evolutionary relationships between a proposed map and a reference map: an existing map of the corresponding orthologous genes or markers in a closely related organism. This has concretely the effect of exploiting, in the process of map selection, the information of marker adjacencies in the related genome when the information provided by the experimental data is not conclusive for the purpose of ordering. In order to compute efficiently the map, we proceed to a reduction of the maximum likelihood estimation to the Traveling Salesman Problem. Experiments on simulated RH datasets as well as on a real RH dataset from the canine RH project show that maps produced using the likelihood defined by the new model are significantly better than maps built using the traditional RH model. AVAILABILITY: The comparative mapping approach is available in the last version of de Givry,S. et al. [(2004) Bioinformatics, 21, 1703-1704, www.inra.fr/mia/T/CarthaGene], a free (the LKH part is free for academic use only) mapping software in C++, including LKH (Helsgaun,K. (2000) Eur. J. Oper. Res., 126, 106-130, www.dat.ruc.dk/keld/research/LKH) for maximum likelihood computation.

Searching RNA motifs and their intermolecular contacts with constraint networks.

MOTIVATION: Searching RNA gene occurrences in genomic sequences is a task whose importance has been renewed by the recent discovery of numerous functional RNA, often interacting with other ligands. Even if several programs exist for RNA motif search, none exists that can represent and solve the problem of searching for occurrences of RNA motifs in interaction with other molecules. RESULTS: We present a constraint network formulation of this problem. RNA are represented as structured motifs that can occur on more than one sequence and which are related together by possible hybridization. The implemented tool MilPat is used to search for several sRNA families in genomic sequences. Results show that MilPat allows to efficiently search for interacting motifs in large genomic sequences and offers a simple and extensible framework to solve such problems. New and known sRNA are identified as H/ACA candidates in Methanocaldococcus jannaschii. AVAILABILITY: http://carlit.toulouse.inra.fr/MilPaT/MilPat.pl.

SAPHO syndrome of the temporomandibular joint associated with sudden deafness.

We report a case of arthritis of the temporomandibular joint (TMJ) associated with sclerosing osteomyelitis of the mandible and temporal bone, causing deafness. The presence of a palmoplantar pustulosis established the diagnosis of SAPHO syndrome. SAPHO (an acronym referring to synovitis, acne, palmoplantar pustulosis, hyperostosis, and osteitis) syndrome is defined by the association of characteristic osteoarticular and dermatologic manifestations, with diffuse sclerosing osteomyelitis of the mandible being a part of this entity. We review the literature of SAPHO syndrome with mandibular manifestations and discuss the mechanisms of inflammatory spread from the TMJ to the cochlea. To our knowledge, this is the first description of skull base involvement in a patient with SAPHO syndrome leading to sudden deafness.

[Magnetic resonance angiography of the thorax in 2000]. / L'imagerie et l'angiographie par r¿esonance magn¿etique du thorax en l'an 2000.

Over the last five years, magnetic resonance imaging (MRI) has been the scene of explosive developments in many fields. MRI exploration of thoracic vessels, perfusion imaging of the pulmonary parenchyma, cine-MR, and apnea sequences have all seen impressive advances. This improvement has been made possible by progress in data processing and surface coil technology for a better signal-noise ratio. In 2000, indications for thoracic MRI remain limited due to the small number of machines available and the fact that the CT scan can provide superior quality images for the pulmonary parenchyma and for visualizing calcifications. MRI can be a complementary exam for lung cancer work-up in case of suspected invasion of the thoracic cavity or the mediastinum. It is the first intention exam in cases involving the greater vessels, with the exception of emergency situations, the posterior mediastinum, and the heart. We review here the current contribution of MRI in diseases of the chest and discuss perspectives for the future.

Detection of focal hepatic lesions with MR imaging: prospective comparison of T2-weighted fast spin-echo with and without fat suppression, T2-weighted breath-hold fast spin-echo, and gadolinium chelate-enhanced 3D gradient-recalled imaging.

OBJECTIVE: The purpose of this study was to compare breath-hold three-dimensional (3D) rapid gradient-echo (GRE) MR imaging obtained before and after gadolinium chelate injection with T2-weighted fast spin-echo and T2-weighted breath-hold fast spin-echo (BHFSE) MR imaging in the detection of focal hepatic masses. SUBJECTS AND METHODS: Fifty-three patients with 108 focal hepatic masses had, prospectively, MR of the liver at 1.5 T. T2-weighted fast spin-echo (6000/117 [TR/effective TE]; echo train length=16; acquisition time = 3 min 12 sec) images obtained with and without fat suppression, T2-weighted BHFSE (2700/105; echo train length = 20; acquisition time = 22 sec), and 3D rapid GRE images (10.1/1.9/30 degrees [TR/TE/alpha]) obtained during one breath-hold (12 scan locations in 21 sec or 20 scan locations in 32 sec) before and after injection of gadolinium chelate were blindly and independently analyzed in consensus by three readers. RESULTS: Gadolinium chelate-enhanced 3D rapid GRE images allowed depiction of more focal hepatic masses (90 of 108, sensitivity = 83%) than did T2-weighted fast spin-echo with fat suppression images (76 of 108, sensitivity = 70%), T2-weighted fast spin-echo without fat suppression images (74 of 108, sensitivity = 69%), T2-weighted BHFSE images (73 of 108, sensitivity = 68%), and unenhanced 3D rapid GRE images (54 of 108, sensitivity = 50%) (p < .01). No difference in sensitivity was found between the three T2-weighted sequences. CONCLUSION: Gadolinium chelate-enhanced 3D rapid GRE imaging is superior to T2-weighted fast spin-echo images obtained with or without fat suppression for the detection of focal hepatic masses. T2-weighted BHFSE is similar to T2-weighted fast spin-echo images in detecting focal hepatic lesions.

T2-weighted spin-echo MR imaging of the liver: breath-hold fast spin-echo versus non-breath-hold fast spin-echo images with and without fat suppression.

OBJECTIVE: The goal of our study was to compare a T2-weighted breath-hold fast spin-echo (BHSE) technique with T2-weighted non-breath-hold fast spin-echo techniques for imaging the liver. SUBJECTS AND METHODS: Thirty-three patients with hepatic lesions had T2-weighted BHSE images obtained in 22 sec and conventional T2-weighted non-breath-hold fast spin-echo images obtained in 3 min 12 sec with and without fat suppression. Images were analyzed quantitatively by measuring the lesion-liver contrast, spleen-liver contrast, and signal-to-noise ratios of lesions and qualitatively by evaluating the sharpness of hepatic contours, visibility of intrahepatic vessels and other segmental landmarks, and presence of artifacts. RESULTS: Quantitatively, lesion-liver contrast, spleen-liver contrast, and signal-to-noise ratios obtained with the BHSE technique were inferior to those obtained with fast spin-echo techniques with and without fat suppression (11.2 +/- 7.1 versus 15.4 +/- 10.6 and 14.5 +/- 9.8, p < .001; 5.3 +/- 3.7 versus 8.7 +/- 3.5 and 7.0 +/- 3.8, p < .001; 16.2 +/- 8.2 versus 20.1 +/- 10.9 and 19.7 +/- 9.5, p < .01, respectively; Student's t test). Qualitatively, image artifacts and intrahepatic vessel depiction on BHSE images were similar to those obtained with the fast spin-echo techniques. The BHSE technique was superior to fat-suppressed fast spin-echo technique for showing hepatic contours (p < .01; Wilcoxon signed-rank test). CONCLUSION: The BHSE technique is quantitatively inferior to non-breath-hold fast spin-echo techniques. However, further studies with a surgical standard of reference are needed to compare the three techniques in terms of sensitivity.