MCR-ALS on metabolic networks: Obtaining more meaningful pathways

[EN] With the aim of understanding the flux distributions across a metabolic network, i.e. within living cells, Principal Component Analysis (PCA) has been proposed to obtain a set of orthogonal components (pathways) capturing most of the variance in the flux data. The problems with this method are (i) that no additional information can be included in the model, and (ii) that orthogonality imposes a hard constraint, not always reasonably. To overcome these drawbacks, here we propose to use a more flexible approach such as Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) to obtain this set of biological pathways through the network. By using this method, different constraints can be included in the model, and the same source of variability can be present in different pathways, which is reasonable from a biological standpoint. This work follows a methodology developed for Pichia pastoris cultures grown on different carbon sources, lately presented in González-Martínez et al. (2014). In this paper a different grey modelling approach, which aims to incorporate a priori knowledge through constraints on the modelling algorithms, is applied to the same case of study. The results of both models are compared to show their strengths and weaknesses.Research in this study was partially supported by the Spanish Ministry of Science and Innovation and FEDER funds from the European Union through grants DPI2011-28112-C04-01 and DPI2011-28112-C04-02. The authors are also grateful to Biopolis SL for supporting this research.Folch-Fortuny, A.; Tortajada Serra, M.; Prats-Montalbán, JM.; Llaneras Estrada, F.; Picó Marco, JA.; Ferrer Riquelme, AJ. (2015). MCR-ALS on metabolic networks: Obtaining more meaningful pathways. Chemometrics and Intelligent Laboratory Systems. 142:293-303. https://doi.org/10.1016/j.chemolab.2014.10.004S29330314

A new fossil from the Jurassic of Patagonia reveals the early basicranial evolution and the origins of Crocodyliformes

Extant crocodylians have a limited taxonomic and ecological diversity but they belong to a lineage (Crocodylomorpha) that includes basal and rather generalized species and a highly diverse clade, Crocodyliformes. The latter was among the most successful groups of Mesozoic tetrapods, both in terms of taxonomic and ecological diversity. Crocodyliforms thrived in terrestrial, semiaquatic, and marine environments, and their fossil diversity includes carnivorous, piscivorous, insectivorous, and herbivorous species. This remarkable ecological and trophic diversity is thought only to occur in forms with a completely akinetic skull, characterized by a functionally integrated and tightly sutured braincase-quadrate-palate complex. However, the patterns of evolutionary change that led to the highly modified skull of crocodyliforms and that likely enabled their diversification remain poorly understood. Herein, a new basal crocodylomorph from the Late Jurassic of Patagonia is described, Almadasuchus figarii gen. et sp. nov. The new taxon is known from a well-preserved posterior region of the skull as well as other craniomandibular and postcranial remains. Almadasuchus figarii differs from all other crocodylomorphs in the presence of six autapomorphic features, including the presence of a large lateral notch on the upper temporal bar, an otic shelf of the squamosal that is wider than long, a deep subtriangular concavity on the posterolateral surface of the squamosal, and an elongated pneumatopore on the ventral surface of the quadrate. Phylogenetic analysis focused on the origin of Crocodyliformes places Almadasuchus as the sister group of Crocodyliformes, supported by synapomorphic features of the skull (e.g. subtriangular basisphenoid, absence of basipterygoid process, absence of a sagittal ridge on the frontal, and a flat anterior skull roof with an ornamented dorsal surface). New braincase information provided by Almadasuchus and other crocodylomorphs indicates that most of the modifications on the posterior region of the skull of crocodyliforms, including the strongly sutured braincase, quadrate, and the extensive secondary palate appeared in a stepwise manner, and pre-dated the evolutionary changes in the snout, jaws, and dentition. This indicates that the progressively increased rigidity of the skull provided the structural framework that allowed the great ecological diversification of crocodyliforms during the course of the Mesozoic. The phylogenetic pattern of character acquisition inferred for the strongly sutured (akinetic) skull and the appearance of more diverse feeding behaviours that create high mechanical loads on the skull provides another interesting parallel between the evolution of Mesozoic crocodyliforms and the evolutionary origins of mammals.Fil: Pol, Diego. Museo Paleontológico Egidio Feruglio; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Rauhut, Oliver W. M.. Bayerische Staatssammlung Fur Palaontologie Und Geologie; AlemaniaFil: Lecuona, Agustina. Museo Paleontológico Egidio Feruglio; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Leardi, Juan Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Estudios Andinos; Argentina. Universidad de Buenos Aires; ArgentinaFil: Xu, Xing . Chinese Academy of Science. Institute of Vertebrate Paleontology and Paleoanthropology; ChinaFil: Clark, James M.. George Washington University; Estados Unido

A new cynodont from the Upper Triassic Los Colorados Formation (Argentina, South America) reveals a novel paleobiogeographic context for mammalian ancestors

Probainognathia is a derived lineage of cynodonts which encompass Mammalia as their crown-group. The rich record of probainognathians from the Carnian of Argentina contrasts with their Norian representation, with only one named species. Here we describe a new probainognathian, Tessellatia bonapartei gen. et sp. nov., from the Norian Los Colorados Formation of the Ischigualasto-Villa Unión Basin of Argentina. The new taxon, represented by a partial cranium with associated lower jaws, was analyzed through neutron and X-rays micro-tomography (μCT). The high-resolution neutron μCT data allowed the identification of a unique character combination, including features inaccessible through traditional techniques. We constructed the largest phylogenetic data matrix of non-mammalian cynodonts. The new species and its sister taxon, the Brazilian Therioherpeton cargnini, are recovered as probainognathians, closely related to Mammaliamorpha. We conducted the first quantitative paleobiogeographic analysis of non-mammalian cynodonts, focusing in probainognathians. The results indicate that Probainognathia and Mammaliamorpha originated in southwestern Gondwana (in the Brazilian Paraná Basin), which was an important center of diversification during the Triassic. Finally, the Chinese Lufeng Basin is identified as the ancestral area of Mammaliaformes. These new findings, besides adding to the knowledge of the poorly represented Norian cynodonts from the Los Colorados Formation, are significant to improve our understanding of probainognathian diversity, evolution, and paleobiogeographic history.Fil: Gaetano, Leandro Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Estudios Andinos "Don Pablo Groeber". Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Estudios Andinos "Don Pablo Groeber"; Argentina. University of the Witwatersrand; SudáfricaFil: Abdala, Nestor Fernando. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; Argentina. University of the Witwatersrand; Sudáfrica. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Seoane, Federico Damián. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Estudios Andinos "Don Pablo Groeber". Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Estudios Andinos "Don Pablo Groeber"; ArgentinaFil: Tartaglione, Aureliano. Technische Universitat Munchen. Forschungs-neutronenquelle Heinz Maier-leibnitz (frm Ii); Alemania. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Shulz, M.. Technische Universitat Munchen. Forschungs-neutronenquelle Heinz Maier-leibnitz (frm Ii); AlemaniaFil: Otero, Alejandro. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Departamento Científico de Paleontología de Vertebrados; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Leardi, Juan Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Estudios Andinos "Don Pablo Groeber". Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Estudios Andinos "Don Pablo Groeber"; ArgentinaFil: Apaldetti, Graciela Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de San Juan; ArgentinaFil: Krapovickas, Verónica. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Estudios Andinos "Don Pablo Groeber". Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Estudios Andinos "Don Pablo Groeber"; ArgentinaFil: Steimbach Fonrouge, Eugenio Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Estudios Andinos "Don Pablo Groeber". Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Estudios Andinos "Don Pablo Groeber"; Argentin