Genometrics as an essential tool for the assembly of whole genome sequences: the example of the chromosome of Bifidobacterium longum NCC2705.

BACKGROUND: Analysis of the first reported complete genome sequence of Bifidobacterium longum NCC2705, an actinobacterium colonizing the gastrointestinal tract, uncovered its proteomic relatedness to Streptomyces coelicolor and Mycobacterium tuberculosis. However, a rapid scrutiny by genometric methods revealed a genome organization totally different from all so far sequenced high-GC Gram-positive chromosomes. RESULTS: Generally, the cumulative GC- and ORF orientation skew curves of prokaryotic genomes consist of two linear segments of opposite slope: the minimum and the maximum of the curves correspond to the origin and the terminus of chromosome replication, respectively. However, analyses of the B. longum NCC2705 chromosome yielded six, instead of two, linear segments, while its dnaA locus, usually associated with the origin of replication, was not located at the minimum of the curves. Furthermore, the coorientation of gene transcription with replication was very low. Comparison with closely related actinobacteria strongly suggested that the chromosome of B. longum was misassembled, and the identification of two pairs of relatively long homologous DNA sequences offers the possibility for an alternative genome assembly proposed here below. By genometric criteria, this configuration displays all of the characters common to bacteria, in particular to related high-GC Gram-positives. In addition, it is compatible with the partially sequenced genome of DJO10A B. longum strain. Recently, a corrected sequence of B. longum NCC2705, with a configuration similar to the one proposed here below, has been deposited in GenBank, confirming our predictions. CONCLUSION: Genometric analyses, in conjunction with standard bioinformatic tools and knowledge of bacterial chromosome architecture, represent fast and straightforward methods for the evaluation of chromosome assembly.

Financiamento dos Sistema de Saude

Este Relatório sobre a Saúde no Mundo foi produzido sob a direcção geral de Carissa Etienne, Assistente do Director-Geral, Sistemas e Serviços de Saúde e Anarfi Asamoa-Baah, Director Geral Adjunto. Os redactores principais froam David B Evans, Riku Elovainio e Gary Humphreys; com contribuições de Daniel Chisholm, Joseph Kutzin, Sarah Russell, Priyanka Saksena e Ke Xu. Contribuições sob a forma de caixas de texto e análises foram fornecidos por: Ole Doetinchem, Adelio Fernandes Antunes, Justine Hsu, Chandika K. Indikadahena, Jeremy Lauer, Nathalie van de Maele, Belgacem Sabri, Hossein Salehi, Xenia Scheil-Adlung (ILO) and Karin Stenberg. Sugestões e comentários foram recebidos dos Directores Regionais, Assistentes do Director-Geral e respectivas equipas. Análises, dados e revisões da organização do texto, vários rascunhos ou secções específicas foram fornecidos por (em adição às pessoas jáacima mencionadas): Dele Abegunde, Michael Adelhardt, Hector Arreola, Guitelle Baghdadi-Sabeti, Dina Balabanova, Dorjsuren Bayarsaikhan, Peter Berman, Melanie Bertram, Michael Borowitz, Reinhard Busse, Alexandra Cameron, Guy Carrin, Andrew Cassels, Eleonora Cavagnero, John Connell, David de Ferranti, Don de Savigny, Varatharajan Durairaj, Tamás Evetovits, Josep Figueras, Emma Fitzpatrick, Julio Frenk, Daniela Fuhr, Ramiro Guerrero, Patricia Hernandez Pena, Hans V Hogerzeil, Kathleen Holloway, Melitta Jakab, Elke Jakubowski, Christopher James, Mira Johri, Matthew Jowett, Joses Kirigia, Felicia Knaul, Richard Laing, Nora Markova, Awad Mataria, Inke Mathauer, Don Matheson, Anne Mills, Eduardo Missoni, Laurent Musango, Helena Nygren-Krug, Ariel Pablos-Mendez, Anne-Marie Perucic, Claudia Pescetto, Jean Perrot, Alexander Preker, Magdalena Rathe, Dag Rekve, Ritu Sadana, Rocio Saenz, Thomas Shakespeare, Ian Smith, Peter C Smith, Alaka Singh, Ruben Suarez Berenguela, Tessa Tan-Torres Edejer, Richard Scheffler, Viroj Tangcharoensathien, Fabrizio Tediosi, Sarah Thomson, Ewout van Ginneken, Cornelis van Mosseveld e Julia Watson. A redacção do Relatório foi informada por muitos indivíduos de várias instituições que forneceram documentos de suporte; estes documentos de suporte podem ser encontrados em: http://www.who.int/healthsystems/topics/financing/healthreport/whr_background/en Michael Reid editou as cópias do Relatório, Gaël Kernen produziu as figuras e Evelyn Omukubi forneceu o valioso apoio secretarial e administrativo. O desenho e paginação foi feito por Sophie Guetaneh Aguettant e Cristina Ortiz. Ilustração por Edel Tripp (http://edeltripp.daportfolio.com). A tradução foi realizada por Jorge Cabral e Aurélio Floriano e revista por Aurélio Floriano e Paulo Ferrinho, do Instituto de Higiene e Medicina Tropical, da Universidade Nova de Lisboa - Lisboa, Portugal. A publicação foi produzida com o apoio da Comunidade dos Países de Língua Portuguesa (CPLP), sob autorização do Director Geral da Organização Mundial da Saúde (OMS). As informações contidas neste Relatório não podem, de forma alguma, ser tomadas como a expressão das posições da CPLP

Correction: Topographical Body Fat Distribution Links to Amino Acid and Lipid Metabolism in Healthy Obese Women.

This corrects the article on p. e73445 in vol. 8.]. This corrects the article "Topographical Body Fat Distribution Links to Amino Acid and Lipid Metabolism in Healthy Non-Obese Women" , e73445. There was an error in the title of the article. The correct version of the title in the article is: Topographical Body Fat Distribution Links to Amino Acid and Lipid Metabolism in Healthy Obese Women The correct citation is: Martin F-PJ, Montoliu I, Collino S, Scherer M, Guy P, et al. (2013) Topographical Body Fat Distribution Links to Amino Acid and Lipid Metabolism in Healthy Obese Women. PLoS ONE 8(9): e73445. doi:10.1371/journal.pone.0073445

Post-traumatic stimulus suppressible myoclonus of peripheral origin.

A patient is described who presented with myoclonus of the first dorsal interosseus muscle of the right foot. This myoclonus occurred 18 months after trauma of the cutaneous branch of the deep peroneal nerve on the dorsal aspect of the foot. Tactile stimulation in the dermatome of this nerve, or an anaesthetic block of the deep peroneal nerve stopped the myoclonus. The different innervation between the efferent motor activity responsible for the movements and the sensory afference suppressing it points firmly towards involvement of central connections. However, abolition of the movement by anaesthesia suggests the presence of a peripheral ectopic generator. This finding confirms that focal myoclonus can have its origin in the peripheral nervous system and may be modulated by sensory inputs.

Cardiac Function Assessed by Transesophageal Echocardiography During Pectus Excavatum Repair

Background. We assessed end-diastolic right ventricular (RV) dimensions and left ventricular (LV) ejection fraction by use of intraoperative transesophageal echocardiography before and after surgical correction of pectus excavatum in adults. Methods. A prospective study was conducted including 17 patients undergoing surgical correction of pectus excavatum according to the technique of Ravitch-Shamberger between 1999 and 2004. Intraoperative transesophageal echocardiography was performed under general anesthesia before and after surgery to assess end-diastolic RV dimensions and LV ejection fraction. The end-diastolic RV diameter and area were measured in four-chamber and RV inflow-outflow view, and the RV volume was calculated from these data. The LV was assessed by transgastric short-axis view, and its ejection fraction was calculated by use of the Teichholz formula. Results. The end-diastolic RV diameter, area, and volume all significantly increased after surgery (mean values +/- SD, respectively: 2.4 +/- 0.8 cm versus 3.0 +/- 0.9 cm, p < 0.001; 12.5 +/- 5.2 cm(2) versus 18.4 +/- 7.5 cm(2), p < 0.001; and 21.7 +/- 11.7 mL versus 40.8 +/- 23 mL, p < 0.001). The LV ejection fraction also significantly increased after surgery (58.4% +/- 15% versus 66.2% +/- 6%, p < 0.001). Conclusions. Surgical correction of pectus excavatum according to Ravitch-Shamberger technique results in a significant increase in end-diastolic RV dimensions and a significantly increased LV ejection fraction. (Ann Thorac Surg 2010; 89: 240-4) (C) 2010 by The Society of Thoracic Surgeons

SIMULIT : un modèle de simulation pour l'analyse et la planification de l'activité hospitalière

Le modèle développé à l'Institut universitaire de médecine sociale et préventive de Lausanne utilise un programme informatique pour simuler les mouvements d'entrées et de sorties des hôpitaux de soins généraux. Cette simulation se fonde sur les données récoltées de routine dans les hôpitaux; elle tient notamment compte de certaines variations journalières et saisonnières, du nombre d'entrées, ainsi que du "Case-Mix" de l'hôpital, c'est-à-dire de la répartition des cas selon les groupes cliniques et l'âge des patients.

Study of a Swiss dopa-responsive dystonia family with a deletion in GCH1: redefining DYT14 as DYT5.

OBJECTIVE: To report the study of a multigenerational Swiss family with dopa-responsive dystonia (DRD). METHODS: Clinical investigation was made of available family members, including historical and chart reviews. Subject examinations were video recorded. Genetic analysis included a genome-wide linkage study with microsatellite markers (STR), GTP cyclohydrolase I (GCH1) gene sequencing, and dosage analysis. RESULTS: We evaluated 32 individuals, of whom 6 were clinically diagnosed with DRD, with childhood-onset progressive foot dystonia, later generalizing, followed by parkinsonism in the two older patients. The response to levodopa was very good. Two additional patients had late onset dopa-responsive parkinsonism. Three other subjects had DRD symptoms on historical grounds. We found suggestive linkage to the previously reported DYT14 locus, which excluded GCH1. However, further study with more stringent criteria for disease status attribution showed linkage to a larger region, which included GCH1. No mutation was found in GCH1 by gene sequencing but dosage methods identified a novel heterozygous deletion of exons 3 to 6 of GCH1. The mutation was found in seven subjects. One of the patients with dystonia represented a phenocopy. CONCLUSIONS: This study rules out the previously reported DYT14 locus as a cause of disease, as a novel multiexonic deletion was identified in GCH1. This work highlights the necessity of an accurate clinical diagnosis in linkage studies as well as the need for appropriate allele frequencies, penetrance, and phenocopy estimates. Comprehensive sequencing and dosage analysis of known genes is recommended prior to genome-wide linkage analysis.

Résistances thérapeutiques dans les mouvements anormaux [Resistance to treatment in movement disorders].

Therapeutic strategies for essential tremor (ET) and Parkinson's disease (PD) can be divided into two successive steps, one based on oral medications and the other, more invasive, using pumps or functional neurosurgery. When ET becomes refractory to propranolol, primidone and other, second-choice compounds, deep brain stimulation of the VIM nucleus of the thalamus can be considered. When PD becomes resistant to dopamine replacement therapy using various combinations of dopaminergic agents, then three options can be discussed: first, a subcutaneous apomorphine mini-pump, second, a jejunal levodopa-delivery system by means of percutaneous gastrostomy, and third, bilateral deep brain stimulation of the subthalamic nucleus. The above interventions are successful in about 80% of cases.