Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea

Background: Freshwater planarians are an attractive model for regeneration and stem cell research and have become a promising tool in the field of regenerative medicine. With the availability of a sequenced planarian genome, the recent application of modern genetic and high-throughput tools has resulted in revitalized interest in these animals, long known for their amazing regenerative capabilities, which enable them to regrow even a new head after decapitation. However, a detailed description of the planarian transcriptome is essential for future investigation into regenerative processes using planarians as a model system. Results: In order to complement and improve existing gene annotations, we used a 454 pyrosequencing approach to analyze the transcriptome of the planarian species Schmidtea mediterranea Altogether, 598,435 454-sequencing reads, with an average length of 327 bp, were assembled together with the ~10,000 sequences of the S. mediterranea UniGene set using different similarity cutoffs. The assembly was then mapped onto the current genome data. Remarkably, our Smed454 dataset contains more than 3 million novel transcribed nucleotides sequenced for the first time. A descriptive analysis of planarian splice sites was conducted on those Smed454 contigs that mapped univocally to the current genome assembly. Sequence analysis allowed us to identify genes encoding putative proteins with defined structural properties, such as transmembrane domains. Moreover, we annotated the Smed454 dataset using Gene Ontology, and identified putative homologues of several gene families that may play a key role during regeneration, such as neurotransmitter and hormone receptors, homeobox-containing genes, and genes related to eye function. Conclusions: We report the first planarian transcript dataset, Smed454, as an open resource tool that can be accessed via a web interface. Smed454 contains significant novel sequence information about most expressed genes of S. mediterranea. Analysis of the annotated data promises to contribute to identification of gene families poorly characterized at a functional level. The Smed454 transcriptome data will assist in the molecular characterization of S. mediterranea as a model organism, which will be useful to a broad scientific community.

Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea

Background Freshwater planarians are an attractive model for regeneration and stem cell research and have become a promising tool in the field of regenerative medicine. With the availability of a sequenced planarian genome, the recent application of modern genetic and high-throughput tools has resulted in revitalized interest in these animals, long known for their amazing regenerative capabilities, which enable them to regrow even a new head after decapitation. However, a detailed description of the planarian transcriptome is essential for future investigation into regenerative processes using planarians as a model system. Results In order to complement and improve existing gene annotations, we used a 454 pyrosequencing approach to analyze the transcriptome of the planarian species Schmidtea mediterranea Altogether, 598,435 454-sequencing reads, with an average length of 327 bp, were assembled together with the ~10,000 sequences of the S. mediterranea UniGene set using different similarity cutoffs. The assembly was then mapped onto the current genome data. Remarkably, our Smed454 dataset contains more than 3 million novel transcribed nucleotides sequenced for the first time. A descriptive analysis of planarian splice sites was conducted on those Smed454 contigs that mapped univocally to the current genome assembly. Sequence analysis allowed us to identify genes encoding putative proteins with defined structural properties, such as transmembrane domains. Moreover, we annotated the Smed454 dataset using Gene Ontology, and identified putative homologues of several gene families that may play a key role during regeneration, such as neurotransmitter and hormone receptors, homeobox-containing genes, and genes related to eye function. Conclusions We report the first planarian transcript dataset, Smed454, as an open resource tool that can be accessed via a web interface. Smed454 contains significant novel sequence information about most expressed genes of S. mediterranea. Analysis of the annotated data promises to contribute to identification of gene families poorly characterized at a functional level. The Smed454 transcriptome data will assist in the molecular characterization of S. mediterranea as a model organism, which will be useful to a broad scientific community.

Analysis of gene expression patterns in animals

During my PhD, my aim was to provide new tools to increase our capacity to analyse gene expression patterns, and to study on a large-scale basis the evolution of gene expression in animals. Gene expression patterns (when and where a gene is expressed) are a key feature in understanding gene function, notably in development. It appears clear now that the evolution of developmental processes and of phenotypes is shaped both by evolution at the coding sequence level, and at the gene expression level.Studying gene expression evolution in animals, with complex expression patterns over tissues and developmental time, is still challenging. No tools are available to routinely compare expression patterns between different species, with precision, and on a large-scale basis. Studies on gene expression evolution are therefore performed only on small genes datasets, or using imprecise descriptions of expression patterns.The aim of my PhD was thus to develop and use novel bioinformatics resources, to study the evolution of gene expression. To this end, I developed the database Bgee (Base for Gene Expression Evolution). The approach of Bgee is to transform heterogeneous expression data (ESTs, microarrays, and in-situ hybridizations) into present/absent calls, and to annotate them to standard representations of anatomy and development of different species (anatomical ontologies). An extensive mapping between anatomies of species is then developed based on hypothesis of homology. These precise annotations to anatomies, and this extensive mapping between species, are the major assets of Bgee, and have required the involvement of many co-workers over the years. My main personal contribution is the development and the management of both the Bgee database and the web-application.Bgee is now on its ninth release, and includes an important gene expression dataset for 5 species (human, mouse, drosophila, zebrafish, Xenopus), with the most data from mouse, human and zebrafish. Using these three species, I have conducted an analysis of gene expression evolution after duplication in vertebrates.Gene duplication is thought to be a major source of novelty in evolution, and to participate to speciation. It has been suggested that the evolution of gene expression patterns might participate in the retention of duplicate genes. I performed a large-scale comparison of expression patterns of hundreds of duplicated genes to their singleton ortholog in an outgroup, including both small and large-scale duplicates, in three vertebrate species (human, mouse and zebrafish), and using highly accurate descriptions of expression patterns. My results showed unexpectedly high rates of de novo acquisition of expression domains after duplication (neofunctionalization), at least as high or higher than rates of partitioning of expression domains (subfunctionalization). I found differences in the evolution of expression of small- and large-scale duplicates, with small-scale duplicates more prone to neofunctionalization. Duplicates with neofunctionalization seemed to evolve under more relaxed selective pressure on the coding sequence. Finally, even with abundant and precise expression data, the majority fate I recovered was neither neo- nor subfunctionalization of expression domains, suggesting a major role for other mechanisms in duplicate gene retention.

Contribution of microbial and invertebrate communities to leaf litter colonization in a Mediterranean stream

Leaf litter inputs and retention play an important role in ecosystem functioning in forested streams. We examined colonization of leaves by microbes (bacteria, fungi, and protozoa) and fauna in Fuirosos, an intermittent forested Mediterranean stream. Black poplar (Populus nigra) and plane (Platanus acerifolia) leaf packs were placed in the stream for 4 mo. We measured the biomasses and calculated the densities of bacteria, fungi, protozoa, meiofauna, and macroinvertebrates to determine their dynamics and potential interactions throughout the colonization process. Colonization was strongly correlated with hydrological variability (defined mainly by water temperature and discharge). The 1st week of colonization was characterized by hydrological stability and warm water temperatures, and allocation of C from microbial to invertebrate compartments on the leaf packs was rapid. Clumps of fine particulate organic matter (FPOM) were retained by the leaf packs, and enhanced rapid colonization by microfauna and meiofaunal collector-gatherers (ostracods and copepods). After 2 wk, an autumnal flood caused a 20-fold increase in water flow. Higher discharge and lower water temperature caused FPOM-related fauna to drift away from the packs and modified the subsequent colonization sequence. Fungi showed the highest biomass, with similar values to those recorded at the beginning of the experiment. After 70 d of postflood colonization, fungi decreased to nearly 40% of the total C in the leaf packs, whereas invertebrates became more abundant and accounted for 60% of the C. Natural flood occurrence in Mediterranean streams could be a key factor in the colonization and processing of organic matter.

Regiones limnológicas de Cataluña y ensayo de sistematización de las asociaciones de algas

Los deseos de tipificación y clasificación de las masas de agua dulce han llevado a establecer una tipología tipos de biótopos acuáticos, tipos biológicos de lagos y, al observar la mayor frecuencia con que ciertos tipos se presentan en determinadas regiones por razones climáticas, edáficas (geológicas) y, en menor grado, morfológicas a la llamada limnología regional.

Trichoptera (INSECTA) collected in Mediterranean river basins in the Iberian Peninsula: taxonomic remarks and notes on ecology

As a result of the GUADALMED project, undertaken in Iberian Mediterranean basins, to which were added samples taken by the junior author in the area, we collected numerous caddisfly larvae, pupae and adults. Some larvae were also reared in the lab to obtain adults and allow proper identification. A total of 90 species were identified, which accounts for more than a fourth of the species known in the Iberian Peninsula and Balearic Islands. Here we confirm the presence of doubtful species in the Iberian Peninsula (Glyphotaelius pellucidus) and we expand the distribution range of others (Lype reducta, Micrasema minimum, Limnephilus guadarramicus, Sericostoma pyrenaicum). Moreover, because of the unconformity of morphological larval characteristics with present taxonomical keys (Mesophylax aspersus) or lack of larvae descriptions (Allogamus mortoni, Stenophylax espanioli), here we include some relevant taxonomical aspects that are useful to identify larvae. A brief description of the larva of a possible new species of Hydropsyche (from now on H. gr. instabilis) is also given. Los tricópteros (Insecta) recolectados en las cuencas mediterráneas de la Península Ibérica: notas taxonómicas y requerimientos ecológicos Como resultado de los estudios realizados en el proyecto GUADALMED en las cuencas de los ríos mediterráneos peninsulares y otros muestreos realizados por la primera autora del trabajo se han recolectado numerosas larvas, pupas y adultos de tricópteros. Algunas larvas fueron criadas en el laboratorio para la obtención de adultos y con ello asegurar su identificación. Se han identificado un total de 90 especies que suponen más de una cuarta parte de las especies actualmente conocidas en la Península Ibérica y Baleares. En este trabajo se confirma la presencia, hasta ahora dudosa en la Península Ibérica, de algunas especies (Glyphotaelius pellucidus) y se amplia el área de distribución de otras (Lype reducta, Micrasema minimum, Limnephilus guadarramicus, Sericostoma pyrenaicum). Además, se incluyen algunos aspectos taxonómicos relevantes para la identificación de algunas larvas en futuros estudios, debido a que las claves ya existentes no describen correctamente la larva (Mesophylax aspersus) o porque se trata de larvas sin describir (Allogamus mortoni, Stenophylax espanioli). Se añade también una somera descripción de la larva de una posible nueva especie de Hydropsyche (citada aquí como H. gr. instabilis) y que requiere un estudio más detallado.

A comparison of the energy budgets of two freshwater Pulmonates: Lymnaea peregra (Müller) and Physa acuta (Drap.)

The energy budgets of two freshwater gastropds, Lymnae peregra and Physa acuta, were compared in similar experimental conditions (20ºC, fed ad libitum with 24h-decayed lettuce), and found to differ in several ways. 1) L. Peregra has a higher assimilation efficiency than P. acuta (72% vs 60%). 2) These species assimilate different components of the ingested food: P. acuta uses a smaller, but more energetic part (probably mainly bacteria), whereas L. peregra assimilate a larger, but less energetic part (probably mainly cellulose). 3) L. peregra allocates more of its assimilated energy to oxygene consumption and mucus production (maintenance investments), wheras P. acuta invest more in growth and reproduction (production investments). Such differences are relevant to the natural habitat of these two species: P. acuta colonizes warm, eutrophic and temporary pools, where decaying material constitue the main part of available resources, and where adult mortality is high and impredictible. By contrast, L. peregra is frequently found in colder, oligotrophic and predictible environements, where living primary producers constitute the main part of available resources, and where biotic interactions are important factors of mortality.

Geochemical study of vertebrate fossils from the Upper Cretaceous (Santonian) Csehbanya Formation (Hungary): Evidence for a freshwater habitat of mosasaurs and pycnodont fish

The diverse vertebrate remains from the Upper Cretaceous freshwater settings at Iharkut, Hungary, contain two fossil groups, Pycnodontiformes fish and Mosasauridae that are almost exclusively known from marine palaeo-environments. Hence, their appearance in alluvial sediments is very unusual. Trace element and isotope compositions of the remains have been analyzed to investigate the taphonomy and the ecological differences among the different fossil groups present at Iharkut. All examined fossils have undergone post-depositional diagenetic alteration, which resulted in high concentrations of REE, U, and Fe, together with almost complete homogenization of delta(18)O(CO3) values. Similar REE patterns in different fossils suggest a common origin for all remains, hence the discovered species most likely lived in the same local ecosystem. Despite partial diagenetic overprinting, the delta(18)O(PO4) values of the fossils indicate sufficient taxon-specific isotopic diversity to permit some broad conclusions on the palaeo-environment of the fossils. In particular, it is apparent that the isotopic composition of the Pycnodontiformes fish and Mosasauridae remains is most compatible with a freshwater palaeo-habitat and incompatible with a marine palaeo-environment. In addition, the Sr concentration and isotope data indicate that the Pycnodontiformes and Mosasauridae likely lived predominantly in a freshwater environment and were not simply occasional visitors to the Iharkut river ecosystem. Regarding other fossil groups, high delta(18)O(PO4) values of Alligatoroidea and Iharkutosuchus teeth suggest that these small crocodile species might have inhabited swamps and ponds where the water was relatively rich in (18)O due to evaporation. (c) 2009 Elsevier B.V. All rights reserved.

Perspective: from molecular endocrinology of mouse to genomic endocrinology of animals.

This short perspective explores some ways in which new genomic methodologies impact the study of endocrine signaling. Emphasis is put on the impact of studying species which are not molecular biology models. This opens the door to using knowledge molecular endocrinology in areas of biology as distant as conservation biology, as well as enriching endocrinology with information from biodiversity and natural variation.

Anàlisi dels coneixements intuïtius i del canvi conceptual en infants de parvulari, sobre els animals que viuen el seu entorn

En aquest projecte es reflexiona sobre l’ensenyament de les ciències al parvulari i com els infants aprenent conceptes relacionats amb el regne animal. La ciència escolar classifica la gran diversitat d’espècies que formen aquest regne en dos grans blocs, els vertebrats i els invertebrats, però en els patrons que ens ofereixen els animals per descobrir a ull nu aquestes particularitats són molt complexes d’observar. La visió que tenen els infants de parvulari sobre els animals del seu entorn sovint és molt allunyada de la realitat i els alumnes es creen concepcions alternatives per entendre els animals que observen. En l’estudi es realitza un recull de dades, a l’inici i el final d’una unitat didàctica, analitzant les representacions i les diferents formes de classificació dels animals de l’entorn que utilitzen els infants. Les conclusions són una reflexió sobre el perquè d’aquests coneixements alternatius i la manera de com aconseguir un canvi conceptual.

A Comparative Study: Service Animals and Emotional Support Animals under the Fair Housing Act and the Americans with Disabilities Act & An Overview of Assistance Animal Laws of Select States, April 18, 2010

The Americans with Disabilities Act (ADA) and the Fair Housing Act (FHA) prohibit discrimination on the basis of disability and govern the use of service or emotional support animals in places where pets may not be permitted. However, courts have been struggling with how to define and treat animals that qualify for protection under each law. This has created confusion as to what rights and duties are owed disabled persons and the animals that live with or accompany them. This essay attempts to clarify these two federal laws with regard to service or emotional support animals and the differing parties‘ rights and interests. It also includes an overview of select state laws that govern assistance animals of all types and our recommendations for enhancing the Iowa Civil Rights Act.