Comparative genomic analysis of the odorant-binding protein family in 12 Drosophila genomes: purifying selection and birth-and-death evolution

Background: Chemoreception is a widespread mechanism that is involved in critical biologic processes, including individual and social behavior. The insect peripheral olfactory system comprises three major multigene families: the olfactory receptor (Or), the gustatory receptor (Gr), and the odorant-binding protein (OBP) families. Members of the latter family establish the first contact with the odorants, and thus constitute the first step in the chemosensory transduction pathway.Results: Comparative analysis of the OBP family in 12 Drosophila genomes allowed the identification of 595 genes that encode putative functional and nonfunctional members in extant species, with 43 gene gains and 28 gene losses (15 deletions and 13 pseudogenization events). The evolution of this family shows tandem gene duplication events, progressive divergence in DNA and amino acid sequence, and prevalence of pseudogenization events in external branches of the phylogenetic tree. We observed that the OBP arrangement in clusters is maintained across the Drosophila species and that purifying selection governs the evolution of the family; nevertheless, OBP genes differ in their functional constraints levels. Finally, we detect that the OBP repertoire evolves more rapidly in the specialist lineages of the Drosophila melanogaster group (D. sechellia and D. erecta) than in their closest generalists.Conclusion: Overall, the evolution of the OBP multigene family is consistent with the birth-and-death model. We also found that members of this family exhibit different functional constraints, which is indicative of some functional divergence, and that they might be involved in some of the specialization processes that occurred through the diversification of the Drosophila genus.

Comparative genomics of the odorant-binding and chemosensory protein gene families across the arthropoda: origin and evolutionary history of the chemosensory system

Chemoreception is a biological process essential for the survival of animals, as it allows the recognition of important volatile cues for the detection of food, egg-laying substrates, mates or predators, among other purposes. Furthermore, its role in pheromone detection may contribute to evolutionary processes such as reproductive isolation and speciation. This key role in several vital biological processes makes chemoreception a particularly interesting system for studying the role of natural selection in molecular adaptation. Two major gene families are involved in the perireceptor events of the chemosensory system: the odorant-binding protein (OBP) and chemosensory protein (CSP) families. Here, we have conducted an exhaustive comparative genomic analysis of these gene families in twenty Arthropoda species. We show that the evolution of the OBP and CSP gene families is highly dynamic, with a high number of gains and losses of genes, pseudogenes and independent origins of subfamilies. Taken together, our data clearly support the birth-and-death model for the evolution of these gene families with an overall high gene-turnover rate. Moreover, we show that the genome organization of the two families is significantly more clustered than expected by chance and, more important, that this pattern appears to be actively maintained across the Drosophila phylogeny. Finally, we suggest the homologous nature of the OBP and CSP gene families, dating back their MRCA (most recent common ancestor) to 380¿420 Mya, and we propose a scenario for the origin and diversification of these families.

Average performance analysis of circular and hyperbolic geolocation

A comparative performance analysis of four geolocation methods in terms of their theoretical root mean square positioning errors is provided. Comparison is established in two different ways: strict and average. In the strict type, methods are examined for a particular geometric configuration of base stations(BSs) with respect to mobile position, which determines a givennoise profile affecting the respective time-of-arrival (TOA) or timedifference-of-arrival (TDOA) estimates. In the average type, methodsare evaluated in terms of the expected covariance matrix ofthe position error over an ensemble of random geometries, so thatcomparison is geometry independent. Exact semianalytical equationsand associated lower bounds (depending solely on the noiseprofile) are obtained for the average covariance matrix of the positionerror in terms of the so-called information matrix specific toeach geolocation method. Statistical channel models inferred fromfield trials are used to define realistic prior probabilities for therandom geometries. A final evaluation provides extensive resultsrelating the expected position error to channel model parametersand the number of base stations.

A comparative study of silver amalgam and compomer as retrograde filling materials in periapical surgery

Objective: A comparative study is made of the histological effects of silver amalgam versus compomer (Dyract®) 90 days after placement as retrograde filling materials in experimental animals. Method: Six Beagle dogs were used, with total pulpectomy and orthograde material filling followed by periapical surgery of the 6 upper and 6 lower incisors (for a total of 72 teeth). Thirty-six teeth corresponded to the right side and were filled with the control material (silver amalgam), while the 36 teeth on the left side were filled with the compomer study material (Dyract®). After three months the animals were sacrificed and the histological study was carried out, with evaluation of bone formation, inflammation, and the tissue in contact with the filler material. The results obtained were subjected to a descriptive and comparative statistical analysis (chi-square test). Results: The samples retrogradely filled with compomer showed significantly greater percentage inflammation (76.19% versus 26.66% in the control group). On the other hand, a large proportion of samples with root cement growth were found in the compomer group. Filler material expulsion was also significantly more common when compomer was used. Conclusions: the comparative study of the histological findings showed greater inflammation but also greater root cement growth in the compomer group versus the controls

Genome Biology and Evolution of the Animal Kingdom

Estudi realitzat a partir d’una estada a la Institut J.W. Jenkinson Laboratory for Evolution and Development of the University of Oxford, Regne Unit, entre 2010 i 2012. He estat membre del laboratori del Professor Peter W.H. Holland com a becari post-doctoral Beatriu de Pinós des de setembre de 2010 al setembre de 2012. El nostre projecte de recerca se centra en l'anàlisi genòmic comparatiu del Regne Animal, tot explorant el contingut dels genomes a través de totes les branques de l'arbre dels animals. Totes les referències a les meves publicacions durant aquest post-doc es poden trobar a http://about.me/jordi_paps. Crec que el nombre i la qualitat dels resultats del meu post-doc, un total de 8 publicacions incloent dos articles a la prestigiosa revista Nature, són prova de l'èxit d'aquest post-doc. Prof Peter W. H. Holland (Departament de Zoologia de la Universitat d'Oxford) i jo som coautors de tres articles de genòmica comparativa, resultats directes d'aquest projecte: 1) comparació de families gèniques entre vertebrats invertebrats (Briefings in Functional Genomics), 2) el genoma de l'ostra (publicat a la revista Nature), i 3) els genomes de 6 platihelmints paràsits (acceptat també a Nature). A més, tenim altres 2 treballs en preparació. Un d'ells analitza l'evolució, expressió i funció dels gens Hox al a la tènia Hymenolepis. El perfil fi d'aquests gens clau del desenvolupament esclareix els canvis d'estil de vida dels organismes. A més, durant aquest últim post-doc he participat en diverses col•laboracions, incloent anàlisi de gens d'envelliment a cucs plans, un estudi sobre la filogènia del grup Gastrotricha, una revisió de l'evolució phylum Platyhelminthes, així com un capítol d'un llibre sobre l'evolució dels animals bilaterals. Finalment, gràcies a la beca Beatriu de Pinós, el Prof. Peter W.H. Holland m'ha convidat a formar part del seu equip com un investigador post-doctoral en el seu projecte ERC Advance actual sobre duplicacions genòmiques.

SGP-1: prediction and validation of homologous genes based on sequence alignments

Conventional methods of gene prediction rely on the recognition of DNA-sequence signals, the coding potential or the comparison of a genomic sequence with a cDNA, EST, or protein database. Reasons for limited accuracy in many circumstances are species-specific training and the incompleteness of reference databases. Lately, comparative genome analysis has attracted increasing attention. Several analysis tools that are based on human/mouse comparisons are already available. Here, we present a program for the prediction of protein-coding genes, termed SGP-1 (Syntenic Gene Prediction), which is based on the similarity of homologous genomic sequences. In contrast to most existing tools, the accuracy of SGP-1 depends little on species-specific properties such as codon usage or the nucleotide distribution. SGP-1 may therefore be applied to nonstandard model organisms in vertebrates as well as in plants, without the need for extensive parameter training. In addition to predicting genes in large-scale genomic sequences, the program may be useful to validate gene structure annotations from databases. To this end, SGP-1 output also contains comparisons between predicted and annotated gene structures in HTML format. The program can be accessed via a Web server at http://soft.ice.mpg.de/sgp-1. The source code, written in ANSI C, is available on request from the authors.

Death and resurrection of the human IRGM gene

Immunity-related GTPases (IRG) play an important role in defense against intracellular pathogens. One member of this gene family in humans, IRGM, has been recently implicated as a risk factor for Crohn's disease. We analyzed the detailed structure of this gene family among primates and showed that most of the IRG gene cluster was deleted early in primate evolution, after the divergence of the anthropoids from prosimians ( about 50 million years ago). Comparative sequence analysis of New World and Old World monkey species shows that the single-copy IRGM gene became pseudogenized as a result of an Alu retrotransposition event in the anthropoid common ancestor that disrupted the open reading frame (ORF). We find that the ORF was reestablished as a part of a polymorphic stop codon in the common ancestor of humans and great apes. Expression analysis suggests that this change occurred in conjunction with the insertion of an endogenous retrovirus, which altered the transcription initiation, splicing, and expression profile of IRGM. These data argue that the gene became pseudogenized and was then resurrected through a series of complex structural events and suggest remarkable functional plasticity where alleles experience diverse evolutionary pressures over time. Such dynamism in structure and evolution may be critical for a gene family locked in an arms race with an ever-changing repertoire of intracellular parasites.

Differences based on fine motor behaviour in Parkinson's patients compared to an age matched control group in proprioceptive and visuo-proprioceptive test conditions

Personality differences based on fine motor precision performance were studied in early stage Parkinson's patients and an age-matched control group under two different test conditions: proprioceptive + visual information and proprioceptive information alone. A comparative data analysis for deviations of three measured movement types (transversal, frontal and sagittal) was done for both hands (dominant and non-dominant) with relation to personality dimensions. There were found significant differences between the two groups in decision making dimension and emotionality. After splitting the data for gender subgroups, some significant differences were found for men but not for women. The differences in fine motor task performance varied, being better in some directions for the Parkinson"s patients and worse in others. The findings may suggest that medication has both positive and negative effects on motor performance and provoke personality changes, being more pronounced in men.

The Spanish cadet in the European military context a comparative analysis of the professional socialisation

Research on the attitudes, motivations and social and political behavior of European cadets have been made throughout the last decade. Nowadays Spain also joins those surveys. Thru the analysis of polling data, we can consider the different attitudes of Spanish cadets in relation with the other European ones. The conclusion is that although the Spanish political transition to democracy has not ended already in the military teaching system, there are a lot of similarities among Spanish and European cadets.

Toward a comparative analysis of coming and going verbs in Spanish, German, and Polish

This work deals with coming and going verbs in three typologically distinct languages: a Romance one (Spanish), a Germanic one (German) and a Slavic one (Polish) within Fillmore`s (1966, 1971, 1975, 1982, 1983) framework. On the grounds of data description it is shown that visible linguistic phenomena, such as deixis or Aktionsart related clearly to the coming and going verbs, can be transcended, resorting to the more abstract notion called by the author, following Winston (1987) and Speas and Tenny (2003), “viewpoint”.

A Comparative analysis of oil production setors in Saudi Arabia and the United Arab Emirates

Aquest article s'aplica un enfocament comparatiu de la gestió del sector petrolier en dos països rics en petroli a l'Orient Mitjà: Aràbia Saudita i els Emirats Àrabs Units (EAU). Més explícitament, s'examinen els factors que millor expliquen la variació en les estratègies que han vingut aplicant en el sector des de l'establiment de les seves empreses petrolieres nacionals (NOC). Recorrent a la literatura sobre expropiació / privatització en el camp d'Estudis de l'Energia, en aquest treball es proposa un marc teòric per analitzar la lògica que hi ha al darrera de les diferents formes d'exploració i les estratègies de producció en el sector petrolier. Teòricament, aquesta investigació té com a objectiu avançar en un conjunt d'eines d'anàlisi per abordar millor i entendre els determinants reals del procés de presa de decisions en el upstream. Empíricament, el model es prova en els casos divergents d'Aràbia Saudita i els Emirats Àrabs Units, i una sèrie de lliçons s'han extret. En última instància, aquest treball ha d'augmentar la conscienciació entre els erudits i els polític, tant sobre el poc coneixement que tenim sobre els mecanismes interns que impulsen les estratègies ascendents en el majors estats productor de petroli.

A comparative analysis of two methods for the calculation of electric-field-induced perturbations to molecular vibration

Two common methods of accounting for electric-field-induced perturbations to molecular vibration are analyzed and compared. The first method is based on a perturbation-theoretic treatment and the second on a finite-field treatment. The relationship between the two, which is not immediately apparent, is made by developing an algebraic formalism for the latter. Some of the higher-order terms in this development are documented here for the first time. As well as considering vibrational dipole polarizabilities and hyperpolarizabilities, we also make mention of the vibrational Stark effec

A comparative analysis by means of quantum molecular similarity measures of density distributions derived from conventional ab initio and density functional methods

A procedure based on quantum molecular similarity measures (QMSM) has been used to compare electron densities obtained from conventional ab initio and density functional methodologies at their respective optimized geometries. This method has been applied to a series of small molecules which have experimentally known properties and molecular bonds of diverse degrees of ionicity and covalency. Results show that in most cases the electron densities obtained from density functional methodologies are of a similar quality than post-Hartree-Fock generalized densities. For molecules where Hartree-Fock methodology yields erroneous results, the density functional methodology is shown to yield usually more accurate densities than those provided by the second order Møller-Plesset perturbation theory