Prevalence and resistance mutations of non-B HIV-1 subtypes among immigrants in Southern Spain along the decade 2000-2010.

Most of the non-B HIV-1 subtypes are predominant in Sub-Saharan Africa and India although they have been found worldwide. In the last decade, immigration from these areas has increased considerably in Spain. The objective of this study was to evaluate the prevalence of non-B subtypes circulating in a cohort of HIV-1-infected immigrants in Seville, Southern Spain and to identify drug resistance-associated mutations. METHODS: Complete protease and first 220 codons of the reverse transcriptase coding regions were amplified and sequenced by population sequencing. HIV-1 subtypes were determined using Stanford University Drug Resistance Database, and phylogenetic analysis was performed comparing multiple reported sequences. Drug resistance mutations were defined according to the International AIDS Society-USA. RESULTS: From 2000 to 2010 a total of 1,089 newly diagnosed HIV-1-infected patients were enrolled in our cohort. Of these, 121 were immigrants, of which 98 had ethical approval and informed consent to include in our study. Twenty-nine immigrants (29/98, 29.6%) were infected with non-B subtypes, of which 15/29 (51.7%) were CRF02-AG, mostly from Sub-Saharan Africa, and 2/29 (6.9%) were CRF01-AE from Eastern Europe. A, C, F, J and G subtypes from Eastern Europe, Central-South America and Sub-Saharan Africa were also present. Some others harboured recombinant forms CRF02-AG/CRF01-AE, CRF2-AG/G and F/B, B/C, and K/G, in PR and RT-coding regions. Patients infected with non-B subtypes showed a high frequency of minor protease inhibitor resistance mutations, M36I, L63P, and K20R/I. Only one patient, CRF02_AG, showed major resistance mutation L90M. Major RT inhibitor resistance mutations K70R and A98G were present in one patient with subtype G, L100I in one patient with CRF01_AE, and K103N in another patient with CRF01_AE. Three patients had other mutations such as V118I, E138A and V90I. CONCLUSIONS: The circulation of non-B subtypes has significantly increased in Southern Spain during the last decade, with 29.6% prevalence, in association with demographic changes among immigrants. This could be an issue in the treatment and management of these patients. Resistance mutations have been detected in these patients with a prevalence of 7% among treatment-naïve patients compared with the 21% detected among patients under HAART or during treatment interruption.

A multilevel approach to understanding circadian rhythmicity : social and sleep-dependent effects in ants and mice

Résumé françaisLa majorité des organismes vivants sont soumis à l'alternance du jour et de la nuit, conséquence de la rotation de la terre autour de son axe. Ils ont développé un système interne de mesure du temps, appelé horloge circadienne, leur permettant de s'adapter et de synchroniser leur comportement et leur physiologie aux cycles de lumière. Cette dernière est considérée comme étant le signal majeur entraînant l'horloge interne et. par conséquent, les rythmes journaliers d'éveil et de sommeil. Outre sa régulation circadienne, le sommeil est contrôlé par un processus homéostatique qui détermine son besoin. La contribution de ces deux processus dans le fonctionnement cellulaire du cerveau n'a pas encore été investiguée. La mesure de l'amplitude ainsi que de la prévalence des ondes delta de l'EEG (activité delta) constitue un index très fiable du besoin de sommeil. Il a été démontré que cette activité est génétiquement déterminée et associée à un locus de trait quantitatif situé sur le chromosome 13 de la souris.Grâce à des expériences de privation de sommeil et d'analyses de transcriptome du cerveau dans trois souches de souris présentant diverses réponses à la privation de sommeil, nous avons trouvé que Homerla, localisé dans la région d'intérêt du chromosome 13, est le meilleur marqueur du besoin de sommeil. Homerla est impliqué dans la récupération de l'hyperactivité neuronale induite par le glutamate, grâce à son effet tampon sur le calcium intracellulaire. Une fonction fondamentale du sommeil pourrait donc être de protéger le cerveau et de lui permettre de récupérer après une hyperactivité neuronale imposée par une veille prolongée.De plus, nous avons montré que 2032 transcrits sont exprimés rythmiqueraent dans le cerveau de la souris, parmi lesquels seulement 391 le restent après que les animaux aient été privés de sommeil à différents moments au cours des 24 heures. Cette observation montre clairement que la plupart des changements rythmiques au niveau du transcriptome dépendent du sommeil et non de l'horloge circadienne et souligne ainsi l'importance du sommeil dans la physiologie des mammifères.La plupart des expériences concernant les rythmes circadiens ont été réalisées sur des individus isolés en négligeant l'effet du contexte social sur les comportements circadiens. Les espèces sociales, telles que les fourmis, se caractérisent par une division du travail où une répartition des tâches s'effectue entre ses membres. De plus, certaines d'entre elles doivent être pratiquées en continu comme les soins au couvain tandis que d'autres requièrent une activité rythmique comme le fourragement. Ainsi la fourmi est un excellent modèle pour l'étude de 1 influence du contexte social sur les rythmes circadiens.A ces fins, nous avons décidé d'étudier les rythmes circadiens chez une espèce de fourmi Camponotus fellah et de caractériser au niveau moléculaire son horloge circadienne. Nous avons ainsi développé un système vidéo permettant de suivre l'activité locomotrice de tous les individus d'une colonie. Nos résultats montrent que, bien que la plupart des fourmis soient arythmiques à l'intérieur de la colonie, elles développent d'amples rythmes d'activité en isolation. De plus, ces rythmes disparaissent presque aussitôt que la fourmi est réintroduite dans la colonie. Cette rythmicité observée en isolation semble être générée par l'horloge circadienne car elle persiste en condition constante (obscurité totale). Nous avons ensuite regardé si cette apparente arythmie observée dans la colonie résultait d'un effet masquant des interactions sociales sur les rythmes circadiens d'activité. Nos résultats suggèrent que l'horloge interne est fonctionnelle dans la colonie mais que l'expression de ses rythmes au niveau comportemental est inhibée par les interactions sociales. Les analyses moléculaires du statut de l'horloge dans différents contextes sociaux sont actuellement en cours. Le contexte social semble donc un déterminant majeur du comportement circadien chez la fourmi.AbstractAlmost all living organisms on earth are subjected to the alternance of day and night re-sulting from the rotation of the earth around its axis. They have evolved with an internal timing system, termed the circadian clock, enabling them to adapt and synchronize their behavior and physiology to the daily changes in light and related environmental parame¬ters. Light is thought to be the major cue entraining the circadian clock and consequently the rhythms of rest/activity. In addition to its circadian dependent timing, sleep is reg¬ulated by a homeostatic process that determines its need. The contribution of these two processes in the cellular functioning of the brain has not yet been considered. A highly reliable index of the homeostatic process of sleep is the measure of the amplitude and prevalence of the EEG delta waves (delta activity). It has been shown that sleep need, measured by delta activity, is genetically determined and associated with a Quantitative Trait Locus (QTL) located on the mouse chromosome 13. By using sleep deprivation and brain transcriptome profiling in three inbred mouse strains showing different responses to sleep loss, we found that Homerla, localized within this QTL region is the best transcrip¬tional marker of sleep need. Interestingly Homerla is primarily involved in the recovery from glutamate-induced neuronal hyperactivity by its buffering effect on intracellular cal¬cium. A fundamental function of sleep may therefore reside in the protection and recovery of the brain from a neuronal hyperactivity imposed by prolonged wakefulness.Moreover, time course gene expression experiments showed that 2032 brain tran¬scripts present a rhythmic variation, but only 391 of those remain rhythmic when mice are sleep deprived at four time points around the clock. This finding clearly suggests that most changes in gene transcription over the day are sleep-wake dependent rather than clock dependent and underlines the importance of sleep in mammalian physiology.In the second part of this PhD, I was interested in the social influence on circadian behavior. Most experiments done in the circadian field have been performed on isolated individuals and have therefore ignored the effect of the social context on circadian behav-ior. Eusocial insect species such as ants are characterized by a division of labor: colony tasks are distributed among individuals, some of them requiring continuous activity such as nursing or rhythmic ones such as foraging. Thus ants represent a suitable model to study the influence of the social context on the circadian clock and its output rhythms.The aim of this part was to address the effect of social context on circadian rhythms in the ant species Camponotus fellah and to characterize its circadian clock at the molecu¬lar level. We therefore developed a video tracking system to follow the locomotor activity of all individuals in a colony. Our results show that most ants are arrhythmic within the colony, but develop, when subjected to social isolation, strong rhythms of activity that intriguingly disappear when individuals are reintroduced into the colony. The rhythmicity observed in isolated ants seems to be driven by the circadian clock as it persists under constant conditions (complete darkness). We then tested whether the apparent arrhyth- micity in the colony stemmed from a masking effect of social interactions on circadian rhythms. Indeed, we found that circadian clocks of ants in the colony are functional but their expression at the behavioral level is inhibited by social interactions. The molecular assessment of the circadian clock functional state in the different social context is still under investigation. Our results suggest that social context is a major determinant of circadian behavior in ants.

Treatment rationale and study design for a phase III, double-blind, placebo-controlled study of maintenance pemetrexed plus best supportive care versus best supportive care immediately following induction treatment with pemetrexed plus cisplatin for advanced nonsquamous non-small cell lung cancer.

BACKGROUND: To improve the efficacy of first-line therapy for advanced non-small cell lung cancer (NSCLC), additional maintenance chemotherapy may be given after initial induction chemotherapy in patients who did not progress during the initial treatment, rather than waiting for disease progression to administer second-line treatment. Maintenance therapy may consist of an agent that either was or was not present in the induction regimen. The antifolate pemetrexed is efficacious in combination with cisplatin for first-line treatment of advanced NSCLC and has shown efficacy as a maintenance agent in studies in which it was not included in the induction regimen. We designed a phase III study to determine if pemetrexed maintenance therapy improves progression-free survival (PFS) and overall survival (OS) after cisplatin/pemetrexed induction therapy in patients with advanced nonsquamous NSCLC. Furthermore, since evidence suggests expression levels of thymidylate synthase, the primary target of pemetrexed, may be associated with responsiveness to pemetrexed, translational research will address whether thymidylate synthase expression correlates with efficacy outcomes of pemetrexed. METHODS/DESIGN: Approximately 900 patients will receive four cycles of induction chemotherapy consisting of pemetrexed (500 mg/m2) and cisplatin (75 mg/m2) on day 1 of a 21-day cycle. Patients with an Eastern Cooperative Oncology Group performance status of 0 or 1 who have not progressed during induction therapy will randomly receive (in a 2:1 ratio) one of two double-blind maintenance regimens: pemetrexed (500 mg/m2 on day 1 of a 21-day cycle) plus best supportive care (BSC) or placebo plus BSC. The primary objective is to compare PFS between treatment arms. Secondary objectives include a fully powered analysis of OS, objective tumor response rate, patient-reported outcomes, resource utilization, and toxicity. Tumor specimens for translational research will be obtained from consenting patients before induction treatment, with a second biopsy performed in eligible patients following the induction phase. DISCUSSION: Although using a drug as maintenance therapy that was not used in the induction regimen exposes patients to an agent with a different mechanism of action, evidence suggests that continued use of an agent present in the induction regimen as maintenance therapy enables the identification of patients most likely to benefit from maintenance treatment.

Latitude gradients in melanoma incidence and mortality in the non-Maori population of New Zealand

The variation with latitude of incidence and mortality for cutaneous malignant melanoma (CMM) in the non-Maori population of New Zealand was assessed. For those aged 20 to 74 years, the effects of age, time period, birth-cohort, gender, and region (latitude), and some interactions between them were evaluated by log-linear regression methods. Increasing age-standardized incidence and mortality rates with increasing proximity to the equator were found for men and women. These latitude gradients were greater for males than females. The relative risk of melanoma in the most southern part of New Zealand (latitude 44 degrees S) compared with the most northern region (latitude 36 degrees S) was 0.63 (95 percent confidence interval [CI] = 0.60-0.67) for incidence and 0.76 (CI = 0.68-0.86) for mortality, both genders combined. The mean percentage change in CMM rates per degree of latitude for males was greater than those reported in other published studies. Differences between men and women in melanoma risk with latitude suggest that regional sun-behavior patterns or other risk factors may contribute to the latitude gradient observed.

Frequency and types of human papillomavirus among pregnant and non-pregnant women with human immunodeficiency virus infection in Recife determined by genotyping

Women with human immunodeficiency virus (HIV) infection present a higher risk of infection by the human papillomavirus (HPV) and cervical cancer. To determine HPV genotypes and frequencies among HIV-positive women, an analytical cross-sectional study was carried out on 147 women (51 were pregnant and HIV-positive, 45 pregnant and HIV-negative and 51 HIV-positive and not pregnant), who were attended at a maternity hospital in Recife between April 2006-May 2007. They answered a questionnaire and underwent a gynaecological examination, with samples collected for HPV investigation by PCR, hybrid capture II, oncotic colpocytology (Papanicolau) and colposcopy. The frequency of HPV DNA was 85.3% (122/143), with a high proportion of HPV types that have been identified as high risk for cervical cancer. Among HIV-positive pregnant women, there was an HPV prevalence of 96% (48/50), of whom 60.4% (29/48) were high-risk. HPV 16, 58, 18, 66 and 31 were the most frequent types. Colpocytological abnormalities were observed in 35.3% (18/51) of HIV-positive non-pregnant women, 21.6% (11/51) of HIV-positive pregnant women and 13.3% (6/45) of HIV-negative pregnant women with a predominance of low-level lesions. A high prevalence of HPV infection was identified, especially with the high-risk types 16, 58, 18 and 66. This study identified high-risk HPV types in all three groups examined (HIV-positive pregnant women, HIV-negative pregnant women and HIV-positive not pregnant), characterising its distribution in this setting.

Relationship among epidemiological parameters of six childhood infections in a non-immunized Brazilian community

Epidemiological parameters, such as age-dependent force of infection and average age at infection () were estimated for rubella, varicella, rotavirus A, respiratory syncytial virus, hepatitis A and parvovirus B19 infections for a non-immunized Brazilian community, using the same sera samples. The for the aforementioned diseases were 8.45 years (yr) [95% CI: (7.23, 9.48) yr], 3.90 yr [95% CI: (3.51, 4.28) yr], 1.03 yr [95% CI: (0.96, 1.09) yr], 1.58 yr [95% CI: (1.39, 1.79) yr], 7.17 yr [95% CI: (6.48, 7.80) yr] and 7.43 yr [95% CI: (5.68, 9.59) yr], respectively. The differences between average ages could be explained by factors such as differences in the effectiveness of the protection conferred to newborns by maternally derived antibodies, competition between virus species and age-dependent host susceptibility. Our seroprevalence data may illustrate a case of the above-mentioned mechanisms working together within the same population.

Biology and pathogenicity of "Chlamydia"- related organisms

Abstract : This thesis investigates the pathogenicity and biology of Parachlamydia acanthamoebae and other obligate intracellular bacteria related to chlamydiae. All these Chlamydia-like organisms replicate in amoebae. Some evolved to resist to macrophages and represent possible new agents of respiratory tract infection. Using serological and molecular approaches, we showed that Parachlamydia acanthameobae likely plays a role as an etiological agent of pneumonia [1,2]. We also showed that Parachlamydia was able to enter and survive within pneumocytes and lung fibroblasts [3]. Moreover, we developed an animal model of lung infection in mice, which fulfilled the third and fourth Koch postulate [4]. Given the likely role of Parachlamydia in pneumonia, we studied its antibiotic susceptibility. We showed that Chlamydia-related organisms were resistant to quinolones, mainly due to mutations in the QRDR of gyrA [5]. To have tools to investigate the role of other Chlamydia-related bacteria in pneumonia, we developed immunofluorescence assays and assessed the rate of serological cross-reactivity between all these Chlamydia-related bacteria [6]. We also developed new diagnostic specific PCRs [2,7] and sequenced additional genes that are useful for both taxonomic and diagnostic purposes [8]. Then, we applied these serological and molecular approaches to patients with and without respiratory tract infections. This led to the identification of a possible role of Protochlamydia naegleriophila [7] and of Waddlia chondrophila in pneumonia [1]. A significant part of the thesis also investigated interactions of Parachlamydia with macrophages [9] and the host range of Chlamydia-related bacteria [10]. In conclusion, there are growing body of evidence supporting the role of Chlamydia-like organisms as agents of pneumonia. Further studies are needed to precise their pathogenic role in this setting. The diagnostic tools developed during this thesis will be useful to investigate the role of these strict intracellular bacteria in other diseases in both humans and animals [11,12]. Résumé : Le but de cette thèse est de déterminer le rôle pathogène de Parachlamydia et des bactéries apparentées aux Chlamydia ainsi que d'étudier leur biologie. Parachlamydia acanthamoebae est une bactérie intracellulaire apparentée aux Chlamydia, et qui est résistante non seulement aux amibes mais aussi aux macrophages. Par une approche sérologique et moléculaire, nous avons montré que les bactéries apparentées aux Chlamydia jouent probablement un rôle comme agent de pneumonie [1,2]. De plus, nous avons démontré que P. acanthameobae est capable d'entrer et de survivre dans les pneumocytes et fibroblastes pulmonaires [3]. Nous avons ensuite développé un modèle animal remplissant les troisième et quatrième postulats de Koch [4]. Nous avons aussi démontré que les bactéries apparentées aux Chlamydia sont résistantes aux quinolones, en raison de mutations dans la région QRDR de gyrA [5]. Afin de mieux déterminer le rôle pathogène de ces bactéries, nous avons mis au point des techniques d' immunofluorescence et déterminé la cross-réaction sérologique entre les différentes bactéries apparentées aux Chlamydia [6]. Différentes PCR diagnostiques ont aussi été développées [2,7] et des gènes supplémentaires ont été séquencés, qui seront utiles à la taxonomie ainsi qu'au développement de nouvelles méthodes diagnostiques [8]. Ces méthodes ont été appliquées à des échantillons provenant de patient avec ou sans pneumonie et ont permis l'identification du possible rôle pathogène de Protochlamydia naegleriophila [7] et de Waddlia chondrophila [1]. L'interaction de Parachlamydia avec les macrophages [9] et la permissivité de différentes cellules aux bactéries apparentées aux Chlamydia [10] ont également été étudiés dans le cadre de cette thèse. En conclusion, plusieurs nouveaux éléments viennent renforcer l'hypothèse que les bactéries apparentées aux Chlamydia sont des agents de pneumonies. Cependant, d'autres études doivent être menées pour confirmer leur rôle dans cette maladie. Les méthodes diagnostiques développées ici seront très utiles pour déterminer le rôle pathogène de ces bactéries chez les humains et animaux [11,12]

Non-invasive dry mass determination and monitoring at the single cell level with digital holographic microscopy

Digital holography microscopy (DHM) is an optical microscopy technique which allows recording non-invasively the phase shift induced by living cells with nanometric sensitivity. Here, we exploit the phase signal as an indicator of dry mass (related to the protein concentration). This parameter allows monitoring the protein production rate and its evolution during the cell cycle. ©2008 COPYRIGHT SPIE