SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model

CodeML (part of the PAML package) im- plements a maximum likelihood-based approach to de- tect positive selection on a specific branch of a given phylogenetic tree. While CodeML is widely used, it is very compute-intensive. We present SlimCodeML, an optimized version of CodeML for the branch-site model. Our performance analysis shows that SlimCodeML substantially outperforms CodeML (up to 9.38 times faster), especially for large-scale genomic analyses.

Implementation and evaluation of an internet health site for adolescents in Switzerland.

Ciao is a website specifically designed for young people and focuses mainly on health issues. This report presents the process of setting up the site and a first evaluation undertaken by using two self-administered questionnaires administered via the website itself. It suggests that it is possible to provide young people with authoritative health information and to facilitate their access to counseling and health care facilities by having young people use such a website.

Accumulation of human immunodeficiency virus-specific cytotoxic T lymphocytes away from the predominant site of virus replication during primary infection.

Down-regulation of the initial burst of viremia during primary human immunodeficiency virus (HIV) infection is thought to be mediated predominantly by HIV-specific CD8+ cytotoxic T lymphocytes (CTL). This response is associated with major perturbations in the T cell receptor (TCR) repertoire. To investigate the failure of the cellular immune response to adequately control viral spread and replication and to prevent establishment of HIV infection, changes in the TCR repertoire and in the distribution of virus-specific CTL between blood and lymph node were analyzed in three patients with primary infection. By the combined use of clonotype-specific polymerase chain reaction and analysis of the frequency of in vivo activated HIV-specific CTL, it was shown that HIV-specific CTL clones preferentially accumulated in blood as opposed to lymph node. Accumulation of HIV-specific CTL in blood occurred prior to effective down-regulation of virus replication in both blood and lymph node. These findings should provide new insights into how HIV, and possibly other viruses, elude the immune response of the host during primary infection.

Characterization of the ligand-binding site of the serotonin 5-HT3 receptor: the role of glutamate residues 97, 224, AND 235.

Ligand-gated ion channels of the Cys loop family are receptors for small amine-containing neurotransmitters. Charged amino acids are strongly conserved in the ligand-binding domain of these receptor proteins. To investigate the role of particular residues in ligand binding of the serotonin 5-HT3AS receptor (5-HT3R), glutamate amino acid residues at three different positions, Glu97, Glu224, and Glu235, in the extracellular N-terminal domain were substituted with aspartate and glutamine using site-directed mutagenesis. Wild type and mutant receptor proteins were expressed in HEK293 cells and analyzed by electrophysiology, radioligand binding, fluorescence measurements, and immunochemistry. A structural model of the ligand-binding domain of the 5-HT3R based on the acetylcholine binding protein revealed the position of the mutated amino acids. Our results demonstrate that mutations of Glu97, distant from the ligand-binding site, had little effect on the receptor, whereas mutations Glu224 and Glu235, close to the predicted binding site, are indeed important for ligand binding. Mutations E224Q, E224D, and E235Q decreased EC50 and Kd values 5-20-fold, whereas E235D was functionally expressed at a low level and had a more than 100-fold increased EC50 value. Comparison of the fluorescence properties of a fluorescein-labeled antagonist upon binding to wild type 5-HT3R and E235Q, allowed us to localize Glu235 within a distance of 1 nm around the ligand-binding site, as proposed by our model.

'Dusky Sally': La femme esclave entre histoire et fiction

Au travers d'une étude parallèle de deux femmes esclaves - l'une figure historique, l'autre personnage de fiction - et de la façon dont elles ont été inscrites dans, et surtout hors du récit historique et littéraire américain, cet essai vise d'une part à interroger les biais et les limitations de l'historiographie traditionnelle américaine dans sa représentation de l'esclave, et d'autre part à évaluer le rôle de la littérature dans la critique et la « re-vision » du discours historique. Le roman de Gloria Naylor Mama Day (1988) offre ainsi un détour intéressant pour mettre en lumière les processus discursifs, épistémologiques et idéologiques qui ont permis et perpétué l'absence de femmes comme Sally Hemings, esclave et maîtresse supposée de Thomas Jefferson, dans l'Histoire américaine.Through a parallel discussion of two slave women - the first a historical figure, the second a fiction character - and of the way they have been inscribed in, and indeed out of, the historical and fictional narrative of America's past, this essay aims both to interrogate the biases and limitations of traditional American historiography in its representation of slaves and to evaluate the role of literature in the critique and "re-vision" of historical discourse. Gloria Naylor's novel Mama Day (1988) thus provides an interesting detour to cast light on the discursive, epistemological and ideological processes that have permitted and perpetuated the absence from American History of women like Sally Hemings, Thomas Jefferson's slave and supposed mistress.

Le grand nymphée de Leptis Magna : étude historiographique, urbanistique et architecturale

RESUME en français Centrée sur le grand nymphée de Leptis Magna la recherche met en évidence l'évolution et la signification de ce monument des eaux dans l'une des plus importantes cités africaines de l'époque romaine en mettant en lumière trois thèmes principaux. L'étude historiographique permet tout d'abord d'appréhender, à l'aide des témoignages littéraires des siècles derniers et d'une abondante documentation d'archive, l'histoire de l'édifice de son ensablement à sa remise au jour, puis de suivre les différentes étapes de son dégagement et de sa restauration, mettant ainsi en relief la perception des divers observateurs à l'encontre du monument. L'étude urbanistique permet ensuite de dégager la signification de l'édifice dans la cité par rapport aux autres monuments du secteur aux différentes périodes de son histoire, ainsi que de reconstituer l'approvisionnement en eau de Leptis Magna. Enfin, l'étude architecturale s'intéresse à l'analyse détaillée des structures, permettant la mise en évidence de la conception initiale, du fonctionnement et des transformations du nymphée. Cette dernière approche, qui s'accompagne d'un catalogue circonstancié des éléments du décor, fait intervenir des considérations sur les techniques de constructions, le traitement des blocs d'ornementation et, d'une manière plus générale, sur ('économie du chantier. Cette recherche permet non seulement de reconstituer l'aspect, le rôle et l'histoire du monument et de le replacer dans la série des nymphées romains, mais aussi de percevoir son impact sur les habitants du lieu aux différents moments de son histoire, cherchant ainsi à rejoindre par l'archéologie des considérations sociologiques. THE GREAT SEVERAN NYMPHAEUM OF LEPTIS MAGNA: HISTORIOGRAPHICAL, URBANISTIC AND ARCHITECTURAL STUDY RESUME en anglais Based on the great nymphaeum of Leptis Magna, the research considers the development and significance of this water monument in one of the most important African cities of the Roman period, through three principal aspects. The historiographical study aboards the subject through literary testimony from the last centuries and an abundance of documentary archives, the history of the edifice from its burial to its reconstruction, studying the different stages of its unearthing and its restoration, thus pinpointing perspectives from various observers of the monument. The urban study divulges the significance of the edifice in the city, in comparison with other monuments in the region over different periods of its history, as well as reconstituting Leptis Magna's water supply. Finally, the architectural study undertakes a detailed analysis of the structures, which highlights the conception and the transformations of the nymphaeum, as well as its hydraulic functions. This architectural approach, which is accompanied by a detailed catalogue of the decorative elements, juxtaposes the technical considerations of construction with the ornamental treatment of the marble blocks, accounting for the economical aspects of the site of the nymphaeum. This research proposes not only a consideration of the appearance, the role and the history of the monument and situates it within the series of Roman nymphaea, but also the perception of its impact on the local inhabitants at different moments in its history, looking for accomplish by archaeology some sociological considerations.

Repeated exposure to Lutzomyia intermedia sand fly saliva induces local expression of interferon-inducible genes both at the site of injection in mice and in human blood.

During a blood meal, Lutzomyia intermedia sand flies transmit Leishmania braziliensis, a parasite causing tegumentary leishmaniasis. In experimental leishmaniasis, pre-exposure to saliva of most blood-feeding sand flies results in parasite establishment in absence of any skin damages in mice challenged with dermotropic Leishmania species together with saliva. In contrast, pre-immunization with Lu. intermedia salivary gland sonicate (SGS) results in enhanced skin inflammatory exacerbation upon co-inoculation of Lu. intermedia SGS and L. braziliensis. These data highlight potential unique features of both L. braziliensis and Lu. intermedia. In this study, we investigated the genes modulated by Lu. intermedia SGS immunization to understand their potential impact on the subsequent cutaneous immune response following inoculation of both SGS and L. braziliensis. The cellular recruitment and global gene expression profile was analyzed in mice repeatedly inoculated or not with Lu. intermedia. Microarray gene analysis revealed the upregulation of a distinct set of IFN-inducible genes, an immune signature not seen to the same extent in control animals. Of note this INF-inducible gene set was not induced in SGS pre-immunized mice subsequently co-inoculated with SGS and L. braziliensis. These data suggest the parasite prevented the upregulation of this Lu. intermedia saliva-related immune signature. The presence of these IFN-inducible genes was further analyzed in peripheral blood mononuclear cells (PBMCs) sampled from uninfected human individuals living in a L. braziliensis-endemic region of Brazil thus regularly exposed to Lu. intermedia bites. PBMCs were cultured in presence or absence of Lu. intermedia SGS. Using qRT-PCR we established that the IFN-inducible genes induced in the skin of SGS pre-immunized mice, were also upregulated by SGS in PBMCs from human individuals regularly exposed to Lu. intermedia bites, but not in PBMCs of control subjects. These data demonstrate that repeated exposure to Lu. intermedia SGS induces the expression of potentially host-protective IFN-inducible genes.

Early Cretaceous radiolarians of the Northeast Indian Ocean (leg 123 - site 765, site 766 and dsdp site 261) - The Antarctic-Tethys connection

During ODP Leg 123, abundant and well-preserved Neocomian radiolarians were recovered at Site 765 (Argo Abyssal Plain) and Site 766 (lower Exmouth Plateau). Assemblages are characterized by the numerical dominance of a small number of non-tethyan forms and by the scarcity of tethyan taxa. Remarkable contrasts exist between radiolarian assemblages extracted from claystones of Site 765 and reexamined DSDP Site 26 1, and faunas recovered from radiolarian sand layers, only found at Site 765. Clay faunas are unusual in their low diversity of apparently ecologically tolerant (or solution resistant?), ubiquist species, whereas sand faunas are dominated by non-tethyan taxa. Comparisons with Sites 766 and 26 1, as well as sedimentological observations, lead to the conclusion that this faunal contrast resulted from a difference in provenance, rather than from hydraulic sorting or selective dissolution. The ranges of 27 tethyan taxa from Site 765 were compared to the tethyan radiolarian zonation by Jud (1992) by means of the Unitary Associations Method. This calculation allows to directly date the Site 765 assemblages and to estimate the amount of truncation of ranges for tethyan taxa. Over 70% of the already few tethyan species of Site 765, have truncated ranges during the Valanginian-Hauterivian. Radiolarian assemblages recovered from claystones at Sites 765 and 261 in the Argo Basin apparently reflect restricted oceanic conditions during the latest Jurassic-Barremian. Neither sedimentary facies nor faunal associations bear any resemblance to what we know from typical tethyan sequences. We conclude that the Argo Basin was paleoceanographically separated from the Tethys during the Late Jurassic and part of the Early Cretaceous by its position at higher paleolatitudes and/or by enclosing land masses. Assemblages recovered from radiolarian sand layers are dominated by non-tethyan species that are interpreted as circumantarctic. Their first appearance in the late Berriasian-early Valanginian predates the oceanization of the Indo-Australian breakup (M11, late Valanginian), but coincides with a sharp increase in margin-derived pelagic turbidites. The Indo-Australian rift zone and the adjacent margins must have been submerged deeply enough to allow an intermittent influx of circumantarctic cold water into the Argo Basin, creating increased bottom current activity. Cold-water radiolarians carried into the Argo Basin upwelled along the margin, died, and accumulated in radiolarite layers due to winnowing by bottom currents. High rates of faunal change and the sharp increase of bottom current activity are thought to be synchronous with possible pronounced late Berriasian-early Valanginian lowstands in sea level. Hypothetically, both phenomena might have been.caused by a tendency to glaciation on the Antarctic-Australian continent, which was for the first time isolated from the rest of Gondwana by oceanic seaways as a result of Jurassic-Early Cretaceous sea-floor spreading. The absence of most typical tethyan radiolarian species during the Valanginian-Hauterivian is interpreted as reflecting a time of strong influx of circumantarctic cold water following oceanization (M11) and rapid spreading between Southeast India and West Australia. The reappearance and gradual abundance/diversity increase of tethyan taxa, along with the still dominant circumantarctic species are thought to result from overall more equitable climatic conditions during the Barremian-early Aptian and from the establishment of an oceanic connection with the Tethys Ocean during the early Aptian.

A coiled coil trigger site is essential for rapid binding of synaptobrevin to the SNARE acceptor complex.

Exocytosis from synaptic vesicles is driven by stepwise formation of a tight alpha-helical complex between the fusing membranes. The complex is composed of the three SNAREs: synaptobrevin 2, SNAP-25, and syntaxin 1a. An important step in complex formation is fast binding of vesicular synaptobrevin to the preformed syntaxin 1.SNAP-25 dimer. Exactly how this step relates to neurotransmitter release is not well understood. Here, we combined different approaches to gain insights into this reaction. Using computational methods, we identified a stretch in synaptobrevin 2 that may function as a coiled coil "trigger site." This site is also present in many synaptobrevin homologs functioning in other trafficking steps. Point mutations in this stretch inhibited binding to the syntaxin 1.SNAP-25 dimer and slowed fusion of liposomes. Moreover, the point mutations severely inhibited secretion from chromaffin cells. Altogether, this demonstrates that the trigger site in synaptobrevin is crucial for productive SNARE zippering.