Characterization of Non-Trivial Neighborhood Fold Constraints from Protein Sequences using Generalized Topohydrophobicity

Prediction of key features of protein structures, such as secondary structure, solvent accessibility and number of contacts between residues, provides useful structural constraints for comparative modeling, fold recognition, ab-initio fold prediction and detection of remote relationships. In this study, we aim at characterizing the number of non-trivial close neighbors, or long-range contacts of a residue, as a function of its “topohydrophobic” index deduced from multiple sequence alignments and of the secondary structure in which it is embedded. The “topohydrophobic” index is calculated using a two-class distribution of amino acids, based on their mean atom depths. From a large set of structural alignments processed from the FSSP database, we selected 1485 structural sub-families including at least 8 members, with accurate alignments and limited redundancy. We show that residues within helices, even when deeply buried, have few non-trivial neighbors (0–2), whereas β-strand residues clearly exhibit a multimodal behavior, dominated by the local geometry of the tetrahedron (3 non-trivial close neighbors associated with one tetrahedron; 6 with two tetrahedra). This observed behavior allows the distinction, from sequence profiles, between edge and central β-strands within β-sheets. Useful topological constraints on the immediate neighborhood of an amino acid, but also on its correlated solvent accessibility, can thus be derived using this approach, from the simple knowledge of multiple sequence alignments

El fenómeno de las mareas: consideraciones sobre su abordaje en los libros universitarios de física

Se formula un primer análisis exploratorio de las explicaciones encontradas acerca del fenómeno de las mareas, en los libros de texto de física de nivel inicial universitario. Se seleccionaron 8 textos representativos de la enseñanza de la física en este nivel. Se partió de un análisis de contenido sobre el tema y se definieron tres argumentos que sirvieron de ejes para analizar las ideas presentadas en los documentos. Se encontró que, en la mayoría de los textos, el tema se trabaja a partir de ejercicios; en la mayoría, también, se omite la importancia de la caída libre de la Tierra para explicar el doble abultamiento mareal; y, en algunos casos, se confunden los efectos de mareas con los centrífugos producidos por la rotación sobre el propio eje. Se concluye que el abordaje de la temática en los cursos iniciales de física universitaria podría verse dificultado por la falta de profundidad y de claridad de las explicaciones disponibles en los documentos analizados

Leaf optical properties reflect variation in photosynthetic metabolism and its sensitivity to temperature

Researchers from a number of disciplines have long sought the ability to estimate the functional attributes of plant canopies, such as photosynthetic capacity, using remotely sensed data. To date, however, this goal has not been fully realized. In this study, fresh-leaf reflectance spectroscopy (λ=450–2500 nm) and a partial least-squares regression (PLSR) analysis were used to estimate key determinants of photosynthetic capacity—namely the maximum rates of RuBP carboxylation (Vcmax) and regeneration (Jmax)—measured with standard gas exchange techniques on leaves of trembling aspen and eastern cottonwood trees. The trees were grown across an array of glasshouse temperature regimes. The PLSR models yielded accurate and precise estimates of Vcmax and Jmax within and across species and glasshouse temperatures. These predictions were developed using unique contributions from different spectral regions. Most of the wavelengths selected were correlated with known absorption features related to leaf water content, nitrogen concentration, internal structure, and/or photosynthetic enzymes. In a field application of our PLSR models, spectral reflectance data effectively captured the short-term temperature sensitivities of Vcmax and Jmax in aspen foliage. These findings highlight a promising strategy for developing remote sensing methods to characterize dynamic, environmentally sensitive aspects of canopy photosynthetic metabolism at broad scales

Estimation du contenu biochimique d'un couvert végétal à partir de données haute résolution spectrale acquises au niveau satellitaire

* INRA, Centre de Recherche d'Avignon, URD, Domaine St Paul, Site Agroparc, 84914 Avignon cedex 9 Diffusion du document : INRA, Centre de Recherche d'Avignon, URD, Domaine St Paul, Site Agroparc, 84914 Avignon cedex 9 Diplôme : Dr. d'Universit

An exploration on Afro-Puerto Rican Rhythms through the lens of Global Jazz “Introducing The Afro-Caribbean Narrative Into The Conservative French Jazz Education. “

My CE project is an exploration of Afro-Puerto Rican Rhythms through the lens of Global Jazz. Three years ago, I became deeply inspired and drawn to a music rooted in the Afro-Puerto Rican musical traditions, so, spending this year at the Global Jazz Institute researching and studying those rhythms was a way for me to deepen my understanding of it while finding connections with my roots as a French jazz musician. For this project, I had a great part of the research done during this year studying at the Berklee Global Jazz Institute, but also before, while traveling to Puerto Rico and exploring its musical tradition.https://remix.berklee.edu/graduate-studies-global-jazz/1161/thumbnail.jp

Estimation of leaf water content and specific leaf weight from reflectance and transmittance measurements

Specific absorption coefficients for water and dry matter were estimated using a wide range of variation of fresh leaves. The coefficients were derived from the inversion of the PROSPECT leaf optical property model using reflectance and transmittance spectra measured over the 1 300-2 400-nm domain and the corresponding water content (g.cm-2) and specific leaf weight (mass of dry matter per unit leaf.area, g.cm-2). Results show that the estimated values of the specific absorption coefficient for dry matter were not reliable in the strong water absorption bands, although there was agreement with previous studies in spectral regions where water contributed moderately to leaf absorption. We thus proposed to use the values derived by Fourty et al (1996) for dry leaves for the specific absorption coefficient of dry matter. Estimated values of the specific absorption coefficient of water were slightly higher than the values proposed by Curcio and Petty (1951) for pure water. We then investigated the possibility of estimating leaf water content and specific weight by inverting the PROSPECT model using concurrently or separately reflectance and/or transmittance spectra measured over fresh leaves and the specific absorption coefficients proposed by Fourty et al (1996) for dry matter, and Curcio and Petty (1951) for water. Results obtained on the training data set and on an independent data set show accurate and robust estimates of both water content (RMSE = 0.0025 g.cm-2) and specific leaf weight (RMSE = 0.0016 g.cm-2). when reflectance and transmittance were used concurrently. When either reflectance or transmittance measurements were used, the performances of water and dry matter content estimation decreased because of the relaxation of constraints in the inversion process. Possible applications of these results are discussed.Les coefficients spécifiques de l’eau et de la matière sèche sont estimés en inversant le modèle Prospect de propriétés optiques des feuilles sur une collection variée de feuilles fraîches sur lesquelles les contenus en eau (g.cm-2), les masses sèches surfacique (masse de matière sèche par unité de surface de feuille, g.cm-2) et les spectres de réflectance et transmittance dans le domaine 1 300 - 2 400 nm ont été mesurés. Les résultats montrent que les valeurs estimées du coefficient d’absorption spécifique de la matière sèche ne sont pas fiables dans les bandes de forte absorption par l’eau, alors qu’en dehors de ces bandes, un bon accord est observé avec les résultats antérieurs. Nous proposons donc d’utiliser les valeurs de coefficient spécifique d’absorption de Fourty et al (1996) calculées sur des feuilles sèches. Les valeurs estimées du coefficient spécifique d’absorption de l’eau sont légèrement surestimées par rapport aux valeurs proposées par Curcio et Petty (1951). Nous avons ensuite évalué la possibilité d’estimer le contenu en eau et la masse sèche surfacique en inversant le modèle Prospect en utilisant des spectres de réflectance et/ou de transmittance mesurés sur des feuilles fraîches, avec les coefficient spécifiques proposés par Fourty et al pour la matière sèche ou par Curcio et Petty pour l’eau. Les résultats obtenus sur le jeu d’apprentissage et un jeu de données indépendant montrent une bonne estimation du contenu en eau (RMSE = 0,0016 g.cm-2) et de la masse surfacique sèche (RMSE = 0,0016 g.cm-2) quand la réflectance et la transmittance sont utilisées simultanément. En revanche, quand la réflectance ou la transmittance est utilisée seule, la précision des estimations diminue significativement du fait de la réduction des contraintes imposées au processus d’inversion. Les applications possibles de ces résultats sont discutées

On spectral estimates of fresh leaf biochemistry

International audienc

Estimation of leaf water content and specific leaf weight from reflectance and transmittance measurements

International audienc

Signature spectrale d'un couvert sénescent : modélisation et analyse de sensibilité

* INRA Centre d'Avignon, Documentation, Domaine St Paul, Site Agroparc, 84914 Avignon cedex 9 Diffusion du document : INRA Centre d'Avignon, Documentation, Domaine St Paul, Site Agroparc, 84914 Avignon cedex 9National audienc