Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.

With the widespread availability of high-throughput sequencing technologies, sequencing projects have become pervasive in the molecular life sciences. The huge bulk of data generated daily must be analyzed further by biologists with skills in bioinformatics and by "embedded bioinformaticians," i.e., bioinformaticians integrated in wet lab research groups. Thus, students interested in molecular life sciences must be trained in the main steps of genomics: sequencing, assembly, annotation and analysis. To reach that goal, a practical course has been set up for master students at the University of Lausanne: the "Sequence a genome" class. At the beginning of the academic year, a few bacterial species whose genome is unknown are provided to the students, who sequence and assemble the genome(s) and perform manual annotation. Here, we report the progress of the first class from September 2010 to June 2011 and the results obtained by seven master students who specifically assembled and annotated the genome of Estrella lausannensis, an obligate intracellular bacterium related to Chlamydia. The draft genome of Estrella is composed of 29 scaffolds encompassing 2,819,825 bp that encode for 2233 putative proteins. Estrella also possesses a 9136 bp plasmid that encodes for 14 genes, among which we found an integrase and a toxin/antitoxin module. Like all other members of the Chlamydiales order, Estrella possesses a highly conserved type III secretion system, considered as a key virulence factor. The annotation of the Estrella genome also allowed the characterization of the metabolic abilities of this strictly intracellular bacterium. Altogether, the students provided the scientific community with the Estrella genome sequence and a preliminary understanding of the biology of this recently-discovered bacterial genus, while learning to use cutting-edge technologies for sequencing and to perform bioinformatics analyses.

L'exception sportive : champions noirs et culture coloniale (1900-1939)

4e de couv.: Comment la France a-t-elle été colonisée par son Empire ? En traitant du fait national tel qu'il a été modelé par l'idéologie coloniale, ce livre renverse les perspectives. Pour légitimer leurs lointaines conquêtes, la monarchie, l'empire et la république ont conçu, organisé, relayé auprès des Français une culture coloniale. Le cinéma et le théâtre, le sport et l'école, la littérature et la presse, les arts, la publicité, la chanson, sans oublier l'armée, les comités coloniaux, les expositions se sont chargés de diffuser quêtes scientifiques, fascinations exotiques, fiertés patriotiques ainsi qu'intérêts économiques et politiques. A l'heure où la France éprouve la difficulté de rassembler dans un destin commun des mémoires divisées, ce sont les grandes lignes de ce "passé qui ne passe pas" et les méandres d'une utopie coloniale que ce recueil retrace, de la première abolition de l'esclavage aux présents débats sur la "repentance". Une somme.

Selective neurodegeneration induced in rotation-mediated aggregate cell cultures by a transient switch to stationary culture conditions: a potential model to study ischemia-related pathogenic mechanisms.

Aggregating brain cell cultures at an advanced maturational stage (20-21 days in vitro) were subjected for 1-3 h to anaerobic (hypoxic) and/or stationary (ischemic) conditions. After restoration of the normal culture conditions, cell loss was estimated by measuring the release of lactate dehydrogenase as well as the irreversible decrease of cell type-specific enzyme activities, total protein and DNA content. Ischemia for 2 h induced significant neuronal cell death. Hypoxia combined with ischemia affected both neuronal and glial cells to different degrees (GABAergic neurons>cholinergic neurons>astrocytes). Hypoxic and ischemic conditions greatly stimulated the uptake of 2-deoxy-D-glucose, indicating increased glucose consumption. Furthermore, glucose restriction (5.5 mM instead of 25 mM) dramatically increased the susceptibility of neuronal and glial cells to hypoxic and ischemic conditions. Glucose media concentrations below 2 mM caused selective neuronal cell death in otherwise normal culture conditions. GABAergic neurons showed a particularly high sensitivity to glucose restriction, hypoxia, and ischemia. The pattern of ischemia-induced changes in vitro showed many similarities to in vivo findings, suggesting that aggregating brain cell cultures provide a useful in vitro model to study pathogenic mechanisms related to brain ischemia.

Endurance training enhances vasodilation induced by nitric oxide in human skin.

Résumé Il a été démontré que l'exercice physique modifiait le contrôle de la thermorégulation cutané, ce qui se manifeste par une augmentation de la perfusion de la microcirculation de la peau. Pour une même augmentation de température, ce phénomène est plus important chez les sportifs d'endurance que chez les sujets sédentaires. Dans cette étude, nous posons l'hypothèse qu'une composante de cette adaptation peut provenir d'une plus haute capacité des vaisseaux sanguins à répondre à un stimulus vasodilatateur. Pour la tester, nous avons recruté des hommes sains, non fumeurs, soit entraînés (surtout sport d'endurance) ou sédentaires que nous avons partagé en deux classes d'âges (18-35 ans [jeunes] et >50 ans[âgés]). Le flux sanguin cutané était mesuré par un laser-Doppler au niveau de la peau de l'avant-bras. Nous avons alors mesuré la vasodilatation obtenue par les stimuli suivant : Iontophorèse à l'acétylcholine (ACh, un vasodilatateur dépendant de l'endothélium), iontophorèse au nitroprussiate de sodium (SNP, un donneur d'oxyde nitrique) et par libération d'une interruption momentanée du flux artériel huméral (hyperémie réactive). Chez les sujets entraînés, l'effet de l'hyperémie réactive et de l'ACh n'ont pas montré de différence. Par contre, l'augmentation de la perfusion, suivant la iontophorèse de SNP, exprimé en unité de perfusion (PU), était plus importante chez les sujets entraînés que chez les sujets sédentaires (jeunes: 398±54 vs 350±87, p<0.05; âgés: 339±72 vs 307±66, p<0.05). Pour conclure, l'entraînement d'endurance augmente l'effet vasodilatateur de l'oxyde nitrique de la microcirculation cutanée humaine, au moins au niveau de la peau de l'avant-bras. Ces observations ont un intérêt physiologique considérable au vu des résultats d'études récentes qui montrent que le NO sert d'intermédiaire dans la vasodilatation cutanée produite par un stress thermique. Donc, l'augmentation de la bioactivité du NO dans la microcirculation cutanée pourrait être un des mécanismes par lequel l'entraînement physique modifierait le contrôle de la thermorégulation du flux sanguin cutané. Abstract Endurance training modifies the thermoregulatory control of skin blood flow, as manifested by a greater augmentation of skin perfusion for the same increase in core temperature in athletes, in comparison with se-dentary subjects. In this study, we tested the hypothesis that a component of this adaptation might reside in a higher ability of cutaneous blood vessels to respond to vasodilatory stimuli. We recruited healthy nonsmoking males, either endurance trained or sedentary, in two different age ranges (18-35 y and >50 y). Skin blood flow was measured in the forearm skin, using a laser Doppler imager, allowing to record the vasodilatory responses to the following stimuli: iontophoresis of acetylcholine (an endothelium-dependent vasodilator), iontophoresis of sodium nitroprusside (a nitric oxide donor), and release of a temporary interruption of arterial inflow (reactive hyperemia). There was no effect of training on reactive hyperemia or the response to acetylcholine. In contrast, the increase in perfusion following the iontophoresis of sodium nitroprusside, ex-pressed in perfusion units, was larger in trained than in sedentary subjects (younger: 398±54 vs 350±87, p<0.05; older 339±72 vs 307±66, p<0.05). In conclusion, endurance training enhances the vasodilatory effects of nitric oxide in the human dermal microcirculation, at least in forearm skin. These observations have considerable physiologic interest in view of recent data indicating that nitric oxide mediates in part the cutaneous vasodilation induced by heat stress in humans. Therefore, the augmentation of nitric oxide bioactivity in the dermal microcirculation might be one mechanism whereby endurance training modifies the thermoregulatory control of skin blood flow.

β-Glucan Antigenemia Anticipates Diagnosis of Blood Culture-Negative Intraabdominal Candidiasis.

Rationale: Life-threatening intraabdominal candidiasis (IAC) occurs in 30 to 40% of high-risk surgical intensive care unit (ICU) patients. Although early IAC diagnosis is crucial, blood cultures are negative, and the role of Candida score/colonization indexes is not established. Objectives: The aim of this prospective Fungal Infection Network of Switzerland (FUNGINOS) cohort study was to assess accuracy of 1,3-β-d-glucan (BG) antigenemia for diagnosis of IAC. Methods: Four hundred thirty-four consecutive adults with abdominal surgery or acute pancreatitis and ICU stay 72 hours or longer were screened: 89 (20.5%) at high risk for IAC were studied (68 recurrent gastrointestinal tract perforation, 21 acute necrotizing pancreatitis). Diagnostic accuracy of serum BG (Fungitell), Candida score, and colonization indexes was compared. Measurements and Main Results: Fifty-eight of 89 (65%) patients were colonized by Candida; 29 of 89 (33%) presented IAC (27 of 29 with negative blood cultures). Nine hundred twenty-one sera were analyzed (9/patient): median BG was 253 pg/ml (46-9,557) in IAC versus 99 pg/ml (8-440) in colonization (P < 0.01). Sensitivity and specificity of two consecutive BG measurements greater than or equal to 80 pg/ml were 65 and 78%, respectively. In recurrent gastrointestinal tract perforation it was 75 and 77% versus 90 and 38% (Candida score ≥ 3), 79 and 34% (colonization index ≥ 0.5), and 54 and 63% (corrected colonization index ≥ 0.4), respectively. BG positivity anticipated IAC diagnosis (5 d) and antifungal therapy (6 d). Severe sepsis/septic shock and death occurred in 10 of 11 (91%) and 4 of 11 (36%) patients with BG 400 pg/ml or more versus 5 of 18 (28%, P = 0.002) and 1 of 18 (6%, P = 0.05) with BG measurement less than 400 pg/ml. β-Glucan decreased in IAC responding to therapy and increased in nonresponse. Conclusions: BG antigenemia is superior to Candida score and colonization indexes and anticipates diagnosis of blood culture-negative IAC. This proof-of-concept observation in strictly selected high-risk surgical ICU patients deserves investigation of BG-driven preemptive therapy.

Repeated Double-Poling Sprint Training in Hypoxia by Competitive Cross-country Skiers.

PURPOSE: Repeated-sprint training in hypoxia (RSH) was recently shown to improve repeated-sprint ability (RSA) in cycling. This phenomenon is likely to reflect fiber type-dependent, compensatory vasodilation, and therefore, our hypothesis was that RSH is even more beneficial for activities involving upper body muscles, such as double poling during cross-country skiing. METHODS: In a double-blinded fashion, 17 competitive cross-country skiers performed six sessions of repeated sprints (each consisting of four sets of five 10-s sprints, with 20-s intervals of recovery) either in normoxia (RSN, 300 m; FiO2, 20.9%; n = 8) or normobaric hypoxia (RSH, 3000 m; FiO2, 13.8 %; n = 9). Before (pre) and after (post) training, performance was evaluated with an RSA test (10-s all-out sprints-20-s recovery, until peak power output declined by 30%) and a simulated team sprint (team sprint, 3 × 3-min all-out with 3-min rest) on a double-poling ergometer. Triceps brachii oxygenation was measured by near-infrared spectroscopy. RESULTS: From pretraining to posttraining, peak power output in the RSA was increased (P < 0.01) to the same extent (29% ± 13% vs 26% ± 18%, nonsignificant) in RSH and in RSN whereas the number of sprints performed was enhanced in RSH (10.9 ± 5.2 vs 17.1 ± 6.8, P < 0.01) but not in RSN (11.6 ± 5.3 vs 11.7 ± 4.3, nonsignificant). In addition, the amplitude in total hemoglobin variations during sprints throughout RSA rose more in RSH (P < 0.01). Similarly, the average power output during all team sprints improved by 11% ± 9% in RSH and 15% ± 7% in RSN. CONCLUSIONS: Our findings reveal greater improvement in the performance of repeated double-poling sprints, together with larger variations in the perfusion of upper body muscles in RSH compared with those in RSN.

Communication skills training in oncology: a position paper based on a consensus meeting among European experts in 2009.

BACKGROUND: Communication in cancer care has become a major topic of interest. Since there is evidence that ineffective communication affects both patients and oncology clinicians (physicians and nurses), so-called communication skills trainings (CSTs) have been developed over the last decade. While these trainings have been demonstrated to be effective, there is an important heterogeneity with regard to implementation and with regard to evidence of different aspects of CST. METHODS: In order to review and discuss the scientific literature on CST in oncology and to formulate recommendations, the Swiss Cancer League has organised a consensus meeting with European opinion leaders and experts in the field of CST, as well as oncology clinicians, representatives of oncology societies and patient organisations. On the basis of a systematic review and a meta-analysis, recommendations have been developed and agreed upon. RESULTS: Recommendations address (i) the setting, objectives and participants of CST, (ii) its content and pedagogic tools, (iii) organisational aspects, (iv) outcome and (v) future directions and research. CONCLUSION: This consensus meeting, on the basis of European expert opinions and a systematic review and meta-analysis, defines key elements for the current provision and future development and evaluation of CST in oncology.

Epidermal growth factor and bovine growth hormone stimulate differentiation and myelination of brain cell aggregates in culture.

Bovine growth hormone (bGH) and epidermal growth factor (EGF) increased the activity of ornithine decarboxylase (ODC) in brain cell aggregates cultured in a serum-free chemically defined medium. ODC is considered as a marker of cell growth and differentiation. The effect of bGH and EGF on myelination was investigated by measuring two myelin markers, 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP) and myelin basic protein (MBP). EGF treatment at days 2 and 5 caused a dose-dependent increase of both myelin markers at culture day 12. This increase could still be observed at culture day 19, indicating a prolonged action of EGF. The continual presence of bGH in the culture medium produced a large accumulation of MBP at day 19. This effect was dose-dependent and required the presence of triiodothyronine (T3). In contrast, the effect of bGH on CNP activity did not require the presence of T3. This is the first report showing a direct effect of bGH on CNS myelination in vitro and of EGF on both MBP accumulation and ODC activity.

Advancing hypoxic training in team sports: from intermittent hypoxic training to repeated sprint training in hypoxia.

Over the past two decades, intermittent hypoxic training (IHT), that is, a method where athletes live at or near sea level but train under hypoxic conditions, has gained unprecedented popularity. By adding the stress of hypoxia during 'aerobic' or 'anaerobic' interval training, it is believed that IHT would potentiate greater performance improvements compared to similar training at sea level. A thorough analysis of studies including IHT, however, leads to strikingly poor benefits for sea-level performance improvement, compared to the same training method performed in normoxia. Despite the positive molecular adaptations observed after various IHT modalities, the characteristics of optimal training stimulus in hypoxia are still unclear and their functional translation in terms of whole-body performance enhancement is minimal. To overcome some of the inherent limitations of IHT (lower training stimulus due to hypoxia), recent studies have successfully investigated a new training method based on the repetition of short (<30 s) 'all-out' sprints with incomplete recoveries in hypoxia, the so-called repeated sprint training in hypoxia (RSH). The aims of the present review are therefore threefold: first, to summarise the main mechanisms for interval training and repeated sprint training in normoxia. Second, to critically analyse the results of the studies involving high-intensity exercises performed in hypoxia for sea-level performance enhancement by differentiating IHT and RSH. Third, to discuss the potential mechanisms underpinning the effectiveness of those methods, and their inherent limitations, along with the new research avenues surrounding this topic.

Guerre de Troie, guerres des cultures et guerres du Golfe : les usages de "l'Illiade" dans la culture écrite américaine contemporaine

Depuis 1990 et la fin de la Guerre Froide, les Etats-Unis d'Amérique sont devenus la première puissance mondiale, animée par l'idéal de défendre les valeurs occidentale et de répandre la démocratie dans le monde. Or, entre des racines identitaires gréco-romaines empruntées à l'Europe, et les guerres menées au Moyen-Orient contre différents ennemis, la « mission » de l'Amérique suscite critiques et interrogations, et le conflit est autant culturel que militaire. L'Iliade d'Homère au contenu guerrier, érigée par la tradition littéraire en oeuvre fondatrice de l'Occident, offre aux penseurs américains de tous horizons un outil de réflexion propre à éclairer ce présent si inconfortable. A travers l'étude d'un corpus tripartite inédit, ce travail se propose de questionner le rôle d'une oeuvre symbolique de l'Antiquité grecque dans le monde d'aujourd'hui, et débouche sur une réflexion plus large touchant au sens contemporain des études classiques et à la transmission du savoir au sein de la culture populaire. Dans un premier temps, elle examine des ouvrages ou articles à vocation scientifique, mais publiés pour la plupart hors du cadre académique, qui théorisent et expriment les enjeux des guerres des cultures américaines (« culture wars ») divisant conservateurs et libéraux sur la mission véritable d'une éducation libérale. Ces ouvrages se servent également de l'Iliade comme d'un miroir où se reflète les conflits modernes, afin d'atténuer le trouble contemporain en juxtaposant passé et présent. Dans un deuxième temps sont abordés les médias journalistiques et informatiques, à l'aide des résultats obtenus lors de recherches poussées, effectuées dans les archives informatiques des journaux publiés dans les capitales et villes majeures des cinquante Etats américains. De fascinantes comparaisons entre la guerre de Troie et la guerre en Irak y sont notamment construites. Le discours sur l'actualité se développe par le recours à l'Antiquité, et en tire de nombreuses « leçons » destinées au gouvernement américain et à tous les meneurs de guerres. Et dans un troisième temps, deux romans de science-fiction, Ilium (2003) et sa suite Olympos (2005), de Dan Simmons, fournissent un fascinant complément littéraire au reste du corpus. Imprégnés par les culture wars, ils transposent l'Iliade dans un lointain futur et expriment sous une forme nouvelle toutes les interrogations brûlantes qui, aujourd'hui particulièrement, animent une Amérique troublée tant par ses guerres que par la remise en question de son identité occidentale. Par cette réunion de trois domaines dissemblables, ce travail pose aussi de nombreuses questions épistémologiques sur la circulation de l'information, la transformation des savoirs, le flou des frontières entre les genres, la révolution que représente Internet, et la fragmentation progressive de la bulle académique. Il propose également de nombreuses perspectives d'ouverture permettant de poursuivre cette recherche. Car la réception contemporaine de l'Iliade - et de l'Antiquité en général - est un domaine riche et dynamique, qui présente l'avantage - ou l'inconvénient, c'est selon - d'être toujours d'actualité. L'inconfort du présent ne devrait pas empêcher son étude, car les résultats sont extrêmement révélateurs de la véritable relation qu'entretiennent les hommes d'aujourd'hui - et non plus seulement les savants - avec leur passé.