Inconsistent Distances in Substitution Matrices can be Avoided by Properly Handling Hydrophobic Residues

The adequacy of substitution matrices to model evolutionary relationships between amino acid sequences can be numerically evaluated by checking the mathematical property of triangle inequality for all triplets of residues. By converting substitution scores into distances, one can verify that a direct path between two amino acids is shorter than a path passing through a third amino acid in the amino acid space modeled by the matrix. If the triangle inequality is not verified, the intuition is that the evolutionary signal is not well modeled by the matrix, that the space is locally inconsistent and that the matrix construction was probably based on insufficient biological data. Previous analysis on several substitution matrices revealed that the number of triplets violating the triangle inequality increases with sequence divergence. Here, we compare matrices which are dedicated to the alignment of highly divergent proteins. The triangle inequality is tested on several classical substitution matrices as well as in a pair of “complementary” substitution matrices recording the evolutionary pressures inside and outside hydrophobic blocks in protein sequences. The analysis proves the crucial role of hydrophobic residues in substitution matrices dedicated to the alignment of distantly related proteins

Dracula : mécanique des fluides et roman des angoisses circulatoires

La figure du monstre vampirique dans Dracula ex-prime une menace venue des marges. Or, ces marges ont une inscription résolument corporelle. En partant des préoccupations angoissées, toutes victoriennes, persistant à l’égard de la circulation, on s’interrogera sur la visibilité des fluides « du sexe » (sperme, menstrues et lait) dans le roman. L’article démontrera que la « mécanique des fluides » ainsi pensée par Bram Stoker se pose en des termes simples : une esthétique du trouble, où le débordement qui s’incarne, notamment dans les personnages féminins, remplit une fonction cathartique. The vampiric monster in Stoker’s Dracula epitomizes a threat coming from the margins, which happens to be related to the body. Indeed, anxious Victorian concerns persisting about different types of flow lead us to question the concrete visibility of sexual bodily fluids (sperm, menses and milk) in the novel. This study will hence discuss how Stoker’s ”fluid mechanics” conveys an ”aesthetics of trouble”, and how its overflowing serves a cathartic purpose with a direct link to the writing of female protagonists.

SA-Mot: a web server for the identification of motifs of interest extracted from protein loops

The detection of functional motifs is an important step for the determination of protein functions. We present here a new web server SA-Mot (Structural Alphabet Motif) for the extraction and location of structural motifs of interest from protein loops. Contrary to other methods, SA-Mot does not focus only on functional motifs, but it extracts recurrent and conserved structural motifs involved in structural redundancy of loops. SA-Mot uses the structural word notion to extract all structural motifs from uni-dimensional sequences corresponding to loop structures. Then, SA-Mot provides a description of these structural motifs using statistics computed in the loop data set and in SCOP superfamily, sequence and structural parameters. SA-Mot results correspond to an interactive table listing all structural motifs extracted from a target structure and their associated descriptors. Using this information, the users can easily locate loop regions that are important for the protein folding and function. The SA-Mot web server is available at http://sa-mot.mti.univ-paris-diderot.fr

The study of the mercury cycle in polar regions: An international study in Ny-Alesund, Svalbard

Mercury (Hg) is a toxic pollutant and it can be strongly accumulated in the food chain, especially in Polar Regions. This paper presents a part of the work that has been on-going for 3-4 years in Ny-Alesund, Svalbard within the frame of an international collaboration. In Ny-Alesund in spring 2003, the atmospheric chemistry of mercury has been studied so as to better understand the formation of oxidized mercury species in the atmosphere that could be deposited onto snow surfaces. The role of snow as a potential source of mercury to the atmosphere or as a sink has also been approached to better understand the behavior of this metal. Chemical and biological processes seem to play a major role in Hg storage in snow. When melting, snow could be a major source of Hg into the various ecosystems and this toxin could therefore be accumulated into the food chain

A Combinatorial Approach to Detect Coevolved Amino Acid Networks in Protein Families of Variable Divergence

Communication between distant sites often defines the biological role of a protein: amino acid long-range interactions are as important in binding specificity, allosteric regulation and conformational change as residues directly contacting the substrate. The maintaining of functional and structural coupling of long-range interacting residues requires coevolution of these residues. Networks of interaction between coevolved residues can be reconstructed, and from the networks, one can possibly derive insights into functional mechanisms for the protein family. We propose a combinatorial method for mapping conserved networks of amino acid interactions in a protein which is based on the analysis of a set of aligned sequences, the associated distance tree and the combinatorics of its subtrees. The degree of coevolution of all pairs of coevolved residues is identified numerically, and networks are reconstructed with a dedicated clustering algorithm. The method drops the constraints on high sequence divergence limiting the range of applicability of the statistical approaches previously proposed. We apply the method to four protein families where we show an accurate detection of functional networks and the possibility to treat sets of protein sequences of variable divergence

Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins

The surface proteins of human influenza A viruses experience positive selection to escape both human immunity and, more recently, antiviral drug treatments. In bacteria and viruses, immune-escape and drug-resistant phenotypes often appear through a combination of several mutations that have epistatic effects on pathogen fitness. However, the extent and structure of epistasis in influenza viral proteins have not been systematically investigated. Here, we develop a novel statistical method to detect positive epistasis between pairs of sites in a protein, based on the observed temporal patterns of sequence evolution. The method rests on the simple idea that a substitution at one site should rapidly follow a substitution at another site if the sites are positively epistatic. We apply this method to the surface proteins hemagglutinin and neuraminidase of influenza A virus subtypes H3N2 and H1N1. Compared to a non-epistatic null distribution, we detect substantial amounts of epistasis and determine the identities of putatively epistatic pairs of sites. In particular, using sequence data alone, our method identifies epistatic interactions between specific sites in neuraminidase that have recently been demonstrated, in vitro, to confer resistance to the drug oseltamivir; these epistatic interactions are responsible for widespread drug resistance among H1N1 viruses circulating today. This experimental validation demonstrates the predictive power of our method to identify epistatic sites of importance for viral adaptation and public health. We conclude that epistasis plays a large role in shaping the molecular evolution of influenza viruses. In particular, sites with , which would normally not be identified as positively selected, can facilitate viral adaptation through epistatic interactions with their partner sites. The knowledge of specific interactions among sites in influenza proteins may help us to predict the course of antigenic evolution and, consequently, to select more appropriate vaccines and drugs

"Sécrétions Magnifiques" : une esthétique du trouble. Sang menstruel, sperme et lait dans la littérature vampirique

There are three bodily fluids whose recurrence in literature is matched only by their symbolic coherence: sperm, menstrual blood, and milk. These secretions, through their manifestations and occurrences in the texts, question the very fluidity of our socio-cultural representations, with regard, first, to sex (understood both as sexuality and sexual difference – what we may call gender from a social class perspective); then in the face of various notions such as taboo, disgust, or pollution. Thus Dracula by Bram Stoker (1897), as well as later vampiric works springing from this canonical novel, become a privileged vessel for the representation of these fluids. Indeed, the vampire, as a quintessential creature forever in excess of fluids, causes various forms of bodily incontinence relentlessly epitomizing a threat of overflowing otherness. Literary vampires embody the most directly visible avatar of a persisting cultural discomfort regarding bodily fluids. The perspective, therefore, is both aesthetic and comparatist, following a logic drawing just as much from literary and artistic analysis, as it does from political theories issued from gender studies. By relying on a dynamic corpus of text, with an unapologetic subjectivity, the present study aims to sketch a genealogy of these bodily fluids, or, so to speak, of their performative significance, hereby seen as a symptom of "discontent in civilization” highlighted by the vampire’s presence : trouble.Il existe trois fluides corporels dont la récurrence dans la littérature n’a d’égale que leur cohérence symbolique : sperme, sang des menstrues, et lait. Ces sécrétions, par leurs manifestations et occurrences, amènent à remettre en question la liquidité ou fluidité même de nos représentations socioculturelles à l’égard du sexe d’abord (donné à la fois comme sexualité et différence sexuelle de classe – le genre), mais ensuite face aux notions de tabou, de dégoût et de souillure. Or, le roman Dracula de Bram Stoker (1897), ainsi que les œuvres vampiriques héritières de ce texte canonique, se font les vecteurs privilégiés de cette représentation. Le vampire, créature en excès de fluides par excellence, provoque l’incontinence des corps et incarne, sans cesse, une menace de débordement : il est l’avatar le plus directement évident des complexes de culture persistant à l’égard des fluides corporels. La recherche est conduite ici selon une perspective à la fois esthétique et comparatiste, suivant une logique qui emprunte tant à l’analyse littéraire et artistique, qu’aux discours politiques des théories circulant autour des études de genre. En s’appuyant sur un corpus dynamique, élaboré sur mesure et résolument subjectif — la dimension affective étant un angle de vue choisi pour nos recherches — cette étude entend interroger la signification proprement performative des fluides, compris comme symptômes d’un « malaise dans la culture », que le vampire réveille : le trouble

"Sublime Secretions" : aesthetics of trouble. Menstrual blood, sperm and milk. Fluid mechanics in Bram Stoker's Dracula and its literary lineage

Il existe trois fluides corporels dont la récurrence dans la littérature n’a d’égale que leur cohérence symbolique : sperme, sang des menstrues, et lait. Ces sécrétions, par leurs manifestations et occurrences, amènent à remettre en question la liquidité ou fluidité même de nos représentations socioculturelles à l’égard du sexe d’abord (donné à la fois comme sexualité et différence sexuelle de classe – le genre), mais ensuite face aux notions de tabou, de dégoût et de souillure. Or, le roman Dracula de Bram Stoker (1897), ainsi que les œuvres vampiriques héritières de ce texte canonique, se font les vecteurs privilégiés de cette représentation. Le vampire, créature en excès de fluides par excellence, provoque l’incontinence des corps et incarne, sans cesse, une menace de débordement : il est l’avatar le plus directement évident des complexes de culture persistant à l’égard des fluides corporels. La recherche est conduite ici selon une perspective à la fois esthétique et comparatiste, suivant une logique qui emprunte tant à l’analyse littéraire et artistique, qu’aux discours politiques des théories circulant autour des études de genre. En s’appuyant sur un corpus dynamique, élaboré sur mesure et résolument subjectif — la dimension affective étant un angle de vue choisi pour nos recherches — cette étude entend interroger la signification proprement performative des fluides, compris comme symptômes d’un « malaise dans la culture », que le vampire réveille : le trouble.There are three bodily fluids whose recurrence in literature is matched only by their symbolic coherence: sperm, menstrual blood, and milk. These secretions, through their manifestations and occurrences in the texts, question the very fluidity of our socio-cultural representations, with regard, first, to sex (understood both as sexuality and sexual difference – what we may call gender from a social class perspective); then in the face of various notions such as taboo, disgust, or pollution. Thus Dracula by Bram Stoker (1897), as well as later vampiric works springing from this canonical novel, become a privileged vessel for the representation of these fluids. Indeed, the vampire, as a quintessential creature forever in excess of fluids, causes various forms of bodily incontinence relentlessly epitomizing a threat of overflowing otherness. Literary vampires embody the most directly visible avatar of a persisting cultural discomfort regarding bodily fluids. The perspective, therefore, is both aesthetic and comparatist, following a logic drawing just as much from literary and artistic analysis, as it does from political theories issued from gender studies. By relying on a dynamic corpus of text, with an unapologetic subjectivity, the present study aims to sketch a genealogy of these bodily fluids, or, so to speak, of their performative significance, hereby seen as a symptom of "discontent in civilization” highlighted by the vampire’s presence : trouble

As Eve Said to the Serpent : Comme Ève le dit au Serpent

Maël Baussand est artiste photographe et universitaire. Elle travaille sur les fluides corporels. Dans ce texte elle revisite poétiquement la rencontre originelle entre Ève et le Serpent.Art photographer and academic researcher, Maël Baussand’s work focuses primarily on the various bodily fluids of sexual difference in art and literature. This poem explores the mythic encounter of Eve with the Snake

Attention et syntaxe : quelles relations chez les enfants DT, TDAH et TDL?

Notre étude cherche à comprendre comment les différents processus attentionnels influencent les performances en syntaxe complexe chez l’enfant. Notre population d’intérêt se compose d’enfants au développement typique (DT), mais aussi d’enfants présentant un trouble du développement du langage (TDL) ou un trouble déficitaire de l’attention avec ou sans hyperactivité (TDAH). En effet, ces deux populations cliniques sont connues comme ayant des difficultés avérées dans le domaine de l’attention et de la syntaxe. Nous avons administré à chaque enfant une batterie de tests attentionnels et syntaxiques, ainsi qu’une tâche d’amorçage dont le but était d’induire la production de phrases passives. Les résultats montrent tout d’abord des liens corrélationnels entre les performances attentionnelles et syntaxiques pour tous les groupes..