A study of the effect of sartorius transposition on lymph flow after ilioinguinal node dissection.

Ilioinguinal dissection is associated with a high rate of lymphatic complications. Prolonged lymph flow causes greatest concern and preventive strategies are needed. A retrospective study of 28 consecutive patients undergoing groin dissection for melanoma metastases was performed to evaluate the influence of sartorius muscle transposition on lymph flow. Modification of the surgical technique with transposition of the sartorius muscle was not associated with reduced drainage time (P = 0.66). A 2-staged approach, with initial sentinel lymph node resection and lymph node dissection in a second operation, however, lead to shortened duration of the lymph flow (P = 0.01). Prolonged lymphorrhea was more frequent in older (P = 0.03), obese (P = 0.02) patients affected by diabetes mellitus (P = 0.03) and hypertension (P = 0.04).

Psychiatrie [Psychiatry].

The novelties in clinical psychiatry are close to somatic medicine adaptation. The clinical staging concept in psychiatry (as in cancerology) is the result of an early intervention strategy in psychotic disorders. A differentiated mode of understanding of the phases of psychiatric disorders allows a prevention oriented approach. Individualized therapeutic programmes in accordance with specific problematics favors the orientation towards focalised follow-ups, for instance CBT programmes on Internet may be proposed to patients motivated and rather autonomous. Others, on the contrary, less accessible to health care should benefit of the support of a mobile team and specific coaching to return to vocational services. Systematic follow-up of the metabolic syndrome, often induced by atypical antipsychotics, belongs to those basic adjustment processes.

Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds.

Pseudomonas knackmussii B13 was the first strain to be isolated in 1974 that could degrade chlorinated aromatic hydrocarbons. This discovery was the prologue for subsequent characterization of numerous bacterial metabolic pathways, for genetic and biochemical studies, and which spurred ideas for pollutant bioremediation. In this study, we determined the complete genome sequence of B13 using next generation sequencing technologies and optical mapping. Genome annotation indicated that B13 has a variety of metabolic pathways for degrading monoaromatic hydrocarbons including chlorobenzoate, aminophenol, anthranilate and hydroxyquinol, but not polyaromatic compounds. Comparative genome analysis revealed that B13 is closest to Pseudomonas denitrificans and Pseudomonas aeruginosa. The B13 genome contains at least eight genomic islands [prophages and integrative conjugative elements (ICEs)], which were absent in closely related pseudomonads. We confirm that two ICEs are identical copies of the 103 kb self-transmissible element ICEclc that carries the genes for chlorocatechol metabolism. Comparison of ICEclc showed that it is composed of a variable and a 'core' region, which is very conserved among proteobacterial genomes, suggesting a widely distributed family of so far uncharacterized ICE. Resequencing of two spontaneous B13 mutants revealed a number of single nucleotide substitutions, as well as excision of a large 220 kb region and a prophage that drastically change the host metabolic capacity and survivability.

Social and medical vulnerability factors of frequent users at the emergency department: a case-control study

BACKGROUND: Up to 5% of patients presenting to the emergency department (ED) four or more times within a 12 month period represent 21% of total ED visits. In this study we sought to characterize social and medical vulnerability factors of ED frequent users (FUs) and to explore if these factors hold simultaneously. METHODS: We performed a case-control study at Lausanne University Hospital, Switzerland. Patients over 18 years presenting to the ED at least once within the study period (April 2008 toMarch 2009) were included. FUs were defined as patients with four or more ED visits within the previous 12 months. Outcome data were extracted from medical records of the first ED attendance within the study period. Outcomes included basic demographics and social variables, ED admission diagnosis, somatic and psychiatric days hospitalized over 12 months, and having a primary care physician.We calculated the percentage of FUs and non-FUs having at least one social and one medical vulnerability factor. The four chosen social factors included: unemployed and/or dependence on government welfare, institutionalized and/or without fixed residence, either separated, divorced or widowed, and under guardianship. The fourmedical vulnerability factors were: ≥6 somatic days hospitalized, ≥1 psychiatric days hospitalized, ≥5 clinical departments used (all three factors measured over 12 months), and ED admission diagnosis of alcohol and/or drug abuse. Univariate and multivariate logistical regression analyses allowed comparison of two JGIM ABSTRACTS S391 random samples of 354 FUs and 354 non-FUs (statistical power 0.9, alpha 0.05 for all outcomes except gender, country of birth, and insurance type). RESULTS: FUs accounted for 7.7% of ED patients and 24.9% of ED visits. Univariate logistic regression showed that FUs were older (mean age 49.8 vs. 45.2 yrs, p=0.003),more often separated and/or divorced (17.5%vs. 13.9%, p=0.029) or widowed (13.8% vs. 8.8%, p=0.029), and either unemployed or dependent on government welfare (31.3% vs. 13.3%, p<0.001), compared to non-FUs. FUs cumulated more days hospitalized over 12 months (mean number of somatic days per patient 1.0 vs. 0.3, p<0.001; mean number of psychiatric days per patient 0.12 vs. 0.03, p<0.001). The two groups were similar regarding gender distribution (females 51.7% vs. 48.3%). The multivariate linear regression model was based on the six most significant factors identified by univariate analysis The model showed that FUs had more social problems, as they were more likely to be institutionalized or not have a fixed residence (OR 4.62; 95% CI, 1.65 to 12.93), and to be unemployed or dependent on government welfare (OR 2.03; 95% CI, 1.31 to 3.14) compared to non-FUs. FUs were more likely to need medical care, as indicated by involvement of≥5 clinical departments over 12 months (OR 6.2; 95%CI, 3.74 to 10.15), having an ED admission diagnosis of substance abuse (OR 3.23; 95% CI, 1.23 to 8.46) and having a primary care physician (OR 1.70;95%CI, 1.13 to 2.56); however, they were less likely to present with an admission diagnosis of injury (OR 0.64; 95% CI, 0.40 to 1.00) compared to non-FUs. FUs were more likely to combine at least one social with one medical vulnerability factor (38.4% vs. 12.1%, OR 7.74; 95% CI 5.03 to 11.93). CONCLUSIONS: FUs were more likely than non-FUs to have social and medical vulnerability factors and to have multiple factors in combination.

Associations between mood, anxiety or substance use disorders and inflammatory markers after adjustment for multiple covariates in a population-based study.

Inflammation is one possible mechanism underlying the associations between mental disorders and cardiovascular diseases (CVD). However, studies on mental disorders and inflammation have yielded inconsistent results and the majority did not adjust for potential confounding factors. We examined the associations of several pro-inflammatory cytokines (IL-1β, IL-6 and TNF-α) and high sensitive C-reactive protein (hsCRP) with lifetime and current mood, anxiety and substance use disorders (SUD), while adjusting for multiple covariates. The sample included 3719 subjects, randomly selected from the general population, who underwent thorough somatic and psychiatric evaluations. Psychiatric diagnoses were made with a semi-structured interview. Major depressive disorder was subtyped into "atypical", "melancholic", "combined atypical-melancholic" and "unspecified". Associations between inflammatory markers and psychiatric diagnoses were assessed using multiple linear and logistic regression models. Lifetime bipolar disorders and atypical depression were associated with increased levels of hsCRP, but not after multivariate adjustment. After multivariate adjustment, SUD remained associated with increased hsCRP levels in men (β = 0.13 (95% CI: 0.03,0.23)) but not in women. After multivariate adjustment, lifetime combined and unspecified depression were associated with decreased levels of IL-6 (β = -0.27 (-0.51,-0.02); β = -0.19 (-0.34,-0.05), respectively) and TNF-α (β = -0.16 (-0.30,-0.01); β = -0.10 (-0.19,-0.02), respectively), whereas current combined and unspecified depression were associated with decreased levels of hsCRP (β = -0.20 (-0.39,-0.02); β = -0.12 (-0.24,-0.01), respectively). Our data suggest that the significant associations between increased hsCRP levels and mood disorders are mainly attributable to the effects of comorbid disorders, medication as well as behavioral and physical CVRFs.

La lymphadénite à mycobactérie atypique [Lymphadenitis due to atypical mycobacteria]

La lymphadénite est une maladie courante dans l'enfance et un motif fréquent de consultation pédiatrique ou ORL. Elle est habituellement due à une infection des voies respiratoires hautes et est autolimitée. Chez l'enfant présentant une lymphadénite cervicale subaiguë ou chronique qui ne répond pas aux antibiotiques habituels, une infection à mycobactérie atypique doit être évoquée. L'infection touche surtout les enfants en bonne santé entre un et cinq ans. Le diagnostic précoce est essentiel car le traitement de choix est l'exérèse des ganglions atteints, avant l'apparition d'une nécrose cutanée et d'une fistulisation. Cet article revoit les présentations cliniques spécifiques, les méthodes diagnostiques et le traitement des lymphadénites à mycobactéries atypiques. Cervical lymphadenitis is common in childhood and is a frequent source of consultation at the pediatrician's or ENT's office. It is usually caused by a viral upper respiratory tract infection and is self limited. In children with subacute or chronic cervical lymphadenitis which fails to respond to conventional antibiotics, infection due to atypical mycobacteria should always be considered. Infections occur predominantly in an otherwise healthy child of 1 to 5 years of age. The early diagnosis is essential as the treatment of choice is early surgical excision before skin necrosis and fistula occur. This article reviews the specific clinical manifestations, diagnostic tools and treatment of lymphadenitis due to atypical mycobacteria.

PAX5 activates the transcription of the human telomerase reverse transcriptase gene in B cells.

Telomerase is an RNA-dependent DNA polymerase that synthesizes telomeric DNA. Its activity is not detectable in most somatic cells but it is reactivated during tumorigenesis. In most cancers, the combination of hTERT hypermethylation and hypomethylation of a short promoter region is permissive for low-level hTERT transcription. Activated and malignant lymphocytes express high telomerase activity, through a mechanism that seems methylation-independent. The aim of this study was to determine which mechanism is involved in the enhanced expression of hTERT in lymphoid cells. Our data confirm that in B cells, some T cell lymphomas and non-neoplastic lymph nodes, the hTERT promoter is unmethylated. Binding sites for the B cell-specific transcription factor PAX5 were identified downstream of the ATG translational start site through EMSA and ChIP experiments. ChIP assays indicated that the transcriptional activation of hTERT by PAX5 does not involve repression of CTCF binding. In a B cell lymphoma cell line, siRNA-induced knockdown of PAX5 expression repressed hTERT transcription. Moreover, ectopic expression of PAX5 in a telomerase-negative normal fibroblast cell line was found to be sufficient to activate hTERT expression. These data show that activation of hTERT in telomerase-positive B cells is due to a methylation-independent mechanism in which PAX5 plays an important role.

Le xeroderma pigmentosum et ses manifestations oculaires. A propos du premier cas camerounais [Xeroderma pigmentosum and its ocular manifestations. The first case in Cameroon].

We report a case of xeroderma pigmentosum in a 9-year-old back Cameroonian boy. The diagnosis was based on typical clinical presentation of the disease: cutaneous atrophy, hypepigmented macules, and areas of depigmentation on sun exposed regions of the skin. Multiple tumoral lesions were localized on the head. Ocular findings were also present: conjunctival hyperemia, peripheral corneal opacification. Excision of the tumors and potoprotection was proposed for this patient. The role of tribal black African marriage traditions in disease transmission is discussed.

Studying the molecular causes of ageing in ants

RÉSUMÉ DE THÈSE Au cours de ma thèse, je me suis intéressée aux causes physiologiques du vieillissement en utilisant les fourmis comme modèle. Les trois castes de fourmis - les mâles, les ouvrières et les reines - présentent des longévités très différentes, tout en étant génétiquement identiques. Ceci implique que les différences de longévité sont dues à des variations entre castes dans le pattern d'expression de gènes. Mon travail chez la fourmi a consisté d'une part à mettre en place les outils pour identifier de tels gènes à grande échelle, de l'autre à étudier le rôle de gènes et de mécanismes qui affectent la longévité chez d'autres espèces. Pour identifier de nouveaux gènes potentiellement impliqués dans le vieillissement, nous avons développé des puces à ADN. Cette technique permet la comparaison du niveau d'expression de milliers de gènes entre deux échantillons. L'application de cette méthode aux reines et ouvrières adultes nous a jusqu'à présent permis d'identifier neuf gènes surexprimés chez les reines. Trois d'entre eux sont potentiellement impliqués dans le maintien et la réparation du soma, deux processus qui sont supposés avoir un impact crucial sur la longévité. Parmi les mécanismes impliqués dans le vieillissement chez d'autres espèces, nous nous sommes principalement intéressés aux télomères, qui sont les extrémités des chromosomes. Chez les vertébrés, les télomères se raccourcissent à chaque division cellulaire, entre autres parce que l'ADN polymérase ne peut répliquer cette partie des chromosomes en entier. Or des télomères courts entravent la prolifération des cellules et peuvent même induire l'apoptose, ce qui pourrait se répercuter sur la capacité des organismes à régénérer des tissus. J'ai pu montrer que chez les fourmis mâles (la caste qui vit le moins longtemps) les télomères se raccourcissent beaucoup plus vite que chez les reines et les ouvrières. L'explication la plus plausible pour cette différence est que les mâles, étant adapté à une vie très éphémère, n'investissent qu'un minimum d'énergie dans la machinerie de maintenance qui assure le bon fonctionnement des cellules. Ces résultats sont intéressants car ils permettent pour la première fois de faire le lien entre les théories évolutives du vieillissement et la biologie des télomères. THESIS ABSTRACT During my thesis I used ants as a model to study the proximate (i.e., molecular) causes of ageing and lifespan determination. Ant queens, workers and males differ tremendously in lifespan, although all three castes are genetically identical. Importantly, this implies that genes and molecular pathways responsible for modulating lifespan are regulated in a caste-specific manner. To find new genes potentially involved in ageing, we first constructed 371-gene-cDNA microarrays for the ant L. niger. This molecular tool can be used to survey the relative gene expression levels of two samples for thousands of genes simultaneously. By applying this method to adult queens and workers we identified nine genes that are overexpressed in queens. Three of them are putatively involved in somatic maintenance and repair, two processes that have been previously suggested as important for ageing and lifespan determination. We expect to identify many more candidate genes in the near future by using the 9000-gene fire ant microarrays we have recently developed. We also investigated whether factors linked to ageing in other organisms could affect lifespan determination in ants. One project was on telomeres, the ends of linear chromosomes. For various reasons telomeres shorten with every cell division. Since short telomeres can lead to cellular defects such as impaired cell division, telomeres have been hypothesized as playing a role in ageing. We tested whether telomere length in ant somatic tissues correlates with caste-specific lifespan in young adults. The short-lived L. niger mates did indeed have significantly shorter telomeres than the longer-lived queens and workers, probably because telomere attrition is faster in males than in queens and workers. Queens did not, however, have longer telomeres than the shorter-lived workers. These findings are consistent with the idea that telomere length may play a role in ageing under some circumstances, but they also clearly demonstrate that other factors must be involved. We argue that sex-specific telomere length patterns in ants ultimately reflect adaptive differences in the level of somatic maintenance between males and females, and thus create a link between telomere biology and the evolutionary theory of ageing.

Identification of Multiple Mechanisms of Resistance to Vemurafenib in a Patient with BRAFV600E-Mutated Cutaneous Melanoma Successfully Rechallenged after Progression.

PURPOSE: To investigate the mechanism(s) of resistance to the RAF-inhibitor vemurafenib, we conducted a comprehensive analysis of the genetic alterations occurring in metastatic lesions from a patient with a BRAF(V600E)-mutant cutaneous melanoma who, after a first response, underwent subsequent rechallenge with this drug. EXPERIMENTAL DESIGN: We obtained blood and tissue samples from a patient diagnosed with a BRAF(V600E)-mutant cutaneous melanoma that was treated with vemurafenib and achieved a near-complete response. At progression, he received additional lines of chemo/immunotherapy and was successfully rechallenged with vemurafenib. Exome and RNA sequencing were conducted on a pretreatment tumor and two subcutaneous resistant metastases, one that was present at baseline and previously responded to vemurafenib (PV1) and one that occurred de novo after reintroduction of the drug (PV2). A culture established from PV1 was also analyzed. RESULTS: We identified two NRAS-activating somatic mutations, Q61R and Q61K, affecting two main subpopulations in the metastasis PV1 and a BRAF alternative splicing, involving exons 4-10, in the metastasis PV2. These alterations, known to confer resistance to RAF inhibitors, were tumor-specific, mutually exclusive, and were not detected in pretreatment tumor samples. In addition, the oncogenic PIK3CA(H1047R) mutation was detected in a subpopulation of PV1, but this mutation did not seem to play a major role in vemurafenib resistance in this metastasis. CONCLUSIONS: This work describes the coexistence within the same patient of different molecular mechanisms of resistance to vemurafenib affecting different metastatic sites. These findings have direct implications for the clinical management of BRAF-mutant melanoma. Clin Cancer Res; 19(20); 5749-57. ©2013 AACR.

The PsyCoLaus study: methodology and characteristics of the sample of a population-based survey on psychiatric disorders and their association with genetic and cardiovascular risk factors.

ABSTRACT: BACKGROUND: The Psychiatric arm of the population-based CoLaus study (PsyCoLaus) is designed to: 1) establish the prevalence of threshold and subthreshold psychiatric syndromes in the 35 to 66 year-old population of the city of Lausanne (Switzerland); 2) test the validity of postulated definitions for subthreshold mood and anxiety syndromes; 3) determine the associations between psychiatric disorders, personality traits and cardiovascular diseases (CVD), 4) identify genetic variants that can modify the risk for psychiatric disorders and determine whether genetic risk factors are shared between psychiatric disorders and CVD. This paper presents the method as well as somatic and sociodemographic characteristics of the sample. METHODS: All 35 to 66 year-old persons previously selected for the population-based CoLaus survey on risk factors for CVD were asked to participate in a substudy assessing psychiatric conditions. This investigation included the Diagnostic Interview for Genetic Studies to elicit diagnostic criteria for threshold disorders according to DSM-IV and algorithmically defined subthreshold syndromes. Complementary information was gathered on potential risk and protective factors for psychiatric disorders, migraine and on the morbidity of first-degree family members, whereas the collection of DNA and plasma samples was part of the original somatic study (CoLaus). RESULTS: A total of 3,691 individuals completed the psychiatric evaluation (67% participation). The gender distribution of the sample did not differ significantly from that of the general population in the same age range. Although the youngest 5-year band of the cohort was underrepresented and the oldest 5-year band overrepresented, participants of PsyCoLaus and individuals who refused to participate revealed comparable scores on the General Health Questionnaire, a self-rating instrument completed at the somatic exam. CONCLUSIONS: Despite limitations resulting from the relatively low participation in the context of a comprehensive and time-consuming investigation, the PsyCoLaus study should significantly contribute to the current understanding of psychiatric disorders and comorbid somatic conditions by: 1) establishing the clinical relevance of specific psychiatric syndromes below the DSM-IV threshold; 2) determining comorbidity between risk factors for CVD and psychiatric disorders; 3) assessing genetic variants associated with common psychiatric disorders and 4) identifying DNA markers shared between CVD and psychiatric disorders.

Specificities of psychodynamic psychotherapy in the medically ill

Psychodynamic psychotherapy with patients suffering from somatic diseases is based on general principles of psychodynamic understanding, such as the influence of development and biographical elements on patient.s adaptation to illness or the role of defense mechanisms when facing existential threat. However, differences exist, such as the adaptation of the therapeutic setting, which thus loses some of its diagnostic and therapeutic power, or the early emergence of powerful transference, which cannot always be interpreted by the therapist. In addition, psychodynamic psychotherapy in the medically ill has some specificities, which differentiate it from classical psychoanalytic theory. The specificities concern, for example, transference of the medically ill, which is more adequately conceived by concepts of the existential analysis (Daseinsanalyse), or the patient.s loss of a sense of continuity, which needs an understanding beyond psychological theory taking into account philosophical (e.g. phenomenology), anthropological and ethical concepts.

Présentation clinique des carcinomes intraépithéliaux (CIN) et des carcinomes invasive de la conjonctive: analyse de 100 cas

Introduction : Les carcinomes de la conjonctive sont les tumeurs oculaires épithéliales des plus fréquentes. Ces tumeurs peuvent se limiter à la membrane basale ou l'envahir pour devenir des tumeurs invasifs. Le diagnostic différentiel entre tumeurs intra‐épithéliales (CIN) et invasifs est exclusivement fait histologiquement. Le but de la présente étude est de définir les caractéristiques cliniques qui sont en faveur du diagnostic d'une CIN ou d'un carcinome invasif afin de améliorer le traitement. Méthode : étude rétrospective des carcinomes de la conjonctive examinés et traités à la Clinique Ophtalmologique Universitaire de Lausanne. Au total 100 dossiers de patients sont étudiés : divers signes cliniques sont notés et analysé selon le type de tumeur (intra‐épithélial et invasif). Résultats : 20 des tumeurs étudié étaient invasifs et 80 intra‐épihteliales, avec une moyenne d'âge de 65 ans. La lésion conjonctivale était localisée pour 40 cas sur 100 dans la région nasale, 22 temporale, 7 inférieures, 3 supérieurs. La forme gélatineuse de la tumeur se présente dans 36 cas sur 100 avec une fréquence relative de 17% en tumeur invasive et 83% en CIN. La forme nodulaire apparait dans 26 cas sur 100 avec 15% en tumeurs invasive et 85% en CIN. La forme papillaire elle se trouve dans 17 cas sur 100 avec 24% invasif et 76% CIN. 21 cas sur 100 sont de type diffus avec 29% invasif et 71% CIN. La kératine était présente dans 40 cas sur 100 avec 23% dans la tumeur invasive et 77% dans CIN. La cornée était touchée dans 74 cas sur 100 avec 20% des cas invasifs et 80% CIN. La taille la plus commune avec 57 cas sur 100 cas est la petite, 21 cas étaient de taille moyenne et 22 cas de taille volumineuse. La grande partie des tumeurs se présente avec un vasodilatation et 45 tumeurs avaient un vascularisation des muscles rectilignes VxR (18% invasif et 82% CIN), 25 cas avaient une vascularisation conjonctivale VxC (0% invasif et 100% CIN), et 30 cas plutôt une vascularisation mixte VxM (33% invasif et 67% CIN). On a trouvé qu'une vasodilatation de la vascularisation mixte (P=0,0294) est statistiquement significative pour caractériser une tumeur invasive et une vasodilatation de la vascularisation de la conjonctive est indicatif pour diagnostiquer un CIN (P=0,0159). La taille de la tumeur joue aussi un rôle important ; dans notre cas la taille volumineuse est statistiquement significative pour déterminer le risque d'avoir une tumeur invasive (P=0,0234). Conclusion : Pour le moment l'excision de la lésion est la méthode la plus plausible pour différencier les carcinomes de la conjonctive. Différents critères permettent de suspecter si la tumeur est invasive ou un CIN, mais ils ne sont pas suffisamment forts pour baser la décision thérapeutique là dessus.

De novo T cell generation and cell cycle analysis of CD4 and CD8 T cells during HIV-disease

RESUME POUR UN LARGE PUBLIC Parmi les globules blancs, les lymphocytes T 004 jouent un rôle primordial dans la coordination de la réponse immunitaire contre les pathogènes et les lymphocytes T CD8 dans leur élimination. Lors d'une infection par le virus de l'immunodéficience humaine (VIH-1), non seulement les cellules T CD4 sont les principales cibles d'infections, mais aussi elles disparaissent progressivement tout au long de la maladie. Ce phénomène, appelé aussi épuisement des lymphocytes T CD4, est la principale cause provoquant le Syndrome d'Immunodéficience Acquise (SIDA). Malgré de grands efforts de recherche, nous ne sommes toujours pas en mesure de dire si ce phénomène est dû à un défaut dans la production de nouvelles cellules ou à une destruction massive de cellules en circulation. Dans cette étude, nous nous proposions, dans un premier temps, de comparer la production de nouvelles cellules T CD4 et CD8 chez des individus VIH-négatifs et positifs. Les cellules nouvellement produites portent un marqueur commun que l'on appelle TREC et qui est facilement mesurable. En considérant des paramètres cliniques, nous étions en mesure de déterminer le niveau de TRECs de cellules T CD4 et CD8 dans différentes phases de la maladie. De là, nous avons pu déterminer que le niveau de TREC est toujours plus bas dans les cellules T CD8 de patients VIH-positifs comparativement à notre groupe contrôle. Nous avons pu déterminer par une analyse ultérieure que cette différence est due à une forte prolifération de ces cellules chez les patients VIH-positifs, ce qui a pour effet de diluer ce marqueur. En revanche, la production de nouvelles cellules T CD4 chez des patients VIH-positifs est accentuée lors de la phase précoce de la maladie et largement réprimée lors de la phase tardive. Dans un second temps, nous avons effectué une analyse à grande échelle de l'expression de gènes associés à la division cellulaire sur des lymphocytes T CD4 et CD8 d'individus VIH-¬positifs et négatifs, avec comme contrôle des cellules proliférant in vitro. De cette étude, nous avons pu conclure que les cellules T CD8 de patients VIH-positifs étaient en état de prolifération, alors que les lymphocytes T CD4 présentaient des défauts majeurs conduisant à un arrêt de la division cellulaire. Nos résultats montrent que la capacité à produire de nouvelles cellules chez des patients VIH¬positifs reste active longtemps pendant la maladie, mais que l'incapacité des cellules T CD4 à proliférer peut enrayer la reconstitution immunitaire chez ces individus. ABSTRACT The hallmark of HIV-1 infection is the depletion of CD4 T cells. Despite extensive investigation, the mechanisms responsible for the loss of CD4 T cells have been elucidated only partially. In particular, it remains controversial whether CD4 T cell depletion results from a defect in T cell production or from a massive peripheral destruction. In this study, de novo T cell generation has been investigated by measuring T cell receptor rearrangement excision circles (TRECs) on large cohorts of HIV-negative (N=120) and HIV-1 infected (N=298) individuals. Analysis of TREC levels was performed in HIV-infected subjects stratified by the stage of HIV disease based on CD4 T cell counts (early: >500 CD4 T cells/µl; intermediate: <500>200; late: <200) and by age (20 to 60 years, n = 259). Our data show that TREC levels in CD8 T cells were significantly lower in HIV-infected subjects at any stage of disease compared to the control group. In contrast, TREC levels in CD4 T cells were significantly higher in HIV-infected subjects at early stages disease while no significant differences were observed at intermediate stages of the disease and were severely reduced only at late stages of disease. To investigate further the status of cell cycle in peripheral CD4 and CD8 T cells in HIV-1 infections, we determined the pattern of gene expression with the microarray technology. In particular, CD4 and CD8 T cells of HIV-1 infected and HIV-negative subjects were analysed by Cell Cycle cDNA expression array. The patterns of gene expression were compared to in vitro stimulated CD4 and CD8 T cells and this analysis showed that CD8 T cells of HIV-1 infected subjects had a pattern of gene expression very similar to that of in vitro stimulated CD8 T cells thus indicating ongoing cell cycling. In contrast, CD4 T cells of HIV-1 infected subjects displayed a complex pattern of gene expression. In fact, CD4 T cells expressed high levels of genes typically associated with cell activation, but low levels of cell cycle genes. Therefore, these results indicated that activated CD4 T cells of HIV-1 infected subjects were in cell cycle arrest. Taking together these results indicate that thymus function is preserved for long time during HIV- 1 infection and the increase observed in early stage disease may represent a compensatory mechanism to the depletion of CD4 T cells. However, we provide evidence for a cell cycle arrest of peripheral CD4 T cells that may prevent potentially the replenishment of CD4 T cells. RESUME Les mécanismes responsables de la perte des lymphocytes T CD4 lors de l'infection pas VIH n'ont été élucidés que partiellement. Nous ne savons toujours pas si l'épuisement des lymphocytes T CD4 résulte d'un défaut dans la production de cellules ou d'une destruction périphérique massive. Dans cette étude, la production de cellules T a été étudiée en mesurant les cercles d'excision générés lors du réarrangement du récepteur au cellules T (TRECs) chez des individus VIH-négatifs (N=120) et VIH-1 positifs (N=298). L'analyse des niveaux de TREC a été faite chez sujets HIV-infectés en considérant les phases de la maladie sur la base des comptes CD4 (phase précoce: > 500 cellules CD4/µl; intermédiaire: < 500>200; tardive: < 200) et par âge. Nos données démontrent que les niveaux de TRECs des cellules T CD8 étaient significativement plus bas chez les sujets VIH-1 infectés, à tous les stades de la maladie comparativement au groupe contrôle. En revanche, les niveaux de TRECs des cellules T CD4 étaient significativement plus élevés chez les sujets VIH-1 infectés durant la phase précoce de la maladie, tandis qu'aucune différence significative n'était observée durant la phase intermédiaire et étaient très réduits dans la phase tardive. Dans une deuxième partie, nous avons utilisé la technique des biopuces à d'ADN complémentaire pour analyser la régulation du cycle cellulaire chez les lymphocytes T CD4 et CD8 périphériques lors d'une infection au VIH-1. Des profils d'expression ont été déterminés et comparés à ceux de cellules T CD4 et CD8 stimulées in vitro, démontrant que les cellules T CD8 des sujets VIH-positifs avaient un profil d'expression très semblable à celui des cellules stimulées in vitro en prolifération. En revanche, les lymphocytes T CD4 des sujets VIH-1 positifs avaient un profil d'expression de gène plus complexe. En fait, leur profil montrait une sur- expression de gènes associés à une activation cellulaire, mais une sous-expression de ceux induisant une division. Ainsi, ces résultats indiquent que les lymphocytes T CD4 d'individus VIH-positifs présentent des dérégulations qui conduisent à un arrêt du cycle cellulaire. Ces résultats montrent que la fonction thymique est préservée longtemps pendant l'infection au VIH-1 et que l'augmentation de la quantité de TRECs dans la phase précoce de la maladie peut représenter un mécanisme compensatoire à l'épuisement des cellules T CD4. Cependant, nous démontrons aussi un clair dysfonctionnement du cycle cellulaire chez les cellules T CD4 d'individus infectés par VIH-1 ce qui peut enrayer la reconstitution du système immunitaire.

Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds.

Pseudomonas knackmussii B13 was the first strain to be isolated in 1974 that could degrade chlorinated aromatic hydrocarbons. This discovery was the prologue for subsequent characterization of numerous bacterial metabolic pathways, for genetic and biochemical studies, and which spurred ideas for pollutant bioremediation. In this study, we determined the complete genome sequence of B13 using next generation sequencing technologies and optical mapping. Genome annotation indicated that B13 has a variety of metabolic pathways for degrading monoaromatic hydrocarbons including chlorobenzoate, aminophenol, anthranilate and hydroxyquinol, but not polyaromatic compounds. Comparative genome analysis revealed that B13 is closest to Pseudomonas denitrificans and Pseudomonas aeruginosa. The B13 genome contains at least eight genomic islands [prophages and integrative conjugative elements (ICEs)], which were absent in closely related pseudomonads. We confirm that two ICEs are identical copies of the 103 kb self-transmissible element ICEclc that carries the genes for chlorocatechol metabolism. Comparison of ICEclc showed that it is composed of a variable and a 'core' region, which is very conserved among proteobacterial genomes, suggesting a widely distributed family of so far uncharacterized ICE. Resequencing of two spontaneous B13 mutants revealed a number of single nucleotide substitutions, as well as excision of a large 220 kb region and a prophage that drastically change the host metabolic capacity and survivability.