Gene finding in the chicken genome.

BACKGROUND: Despite the continuous production of genome sequence for a number of organisms, reliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly true for genomes for which there is not a large collection of known gene sequences, such as the recently published chicken genome. We used the chicken sequence to test comparative and homology-based gene-finding methods followed by experimental validation as an effective genome annotation method. RESULTS: We performed experimental evaluation by RT-PCR of three different computational gene finders, Ensembl, SGP2 and TWINSCAN, applied to the chicken genome. A Venn diagram was computed and each component of it was evaluated. The results showed that de novo comparative methods can identify up to about 700 chicken genes with no previous evidence of expression, and can correctly extend about 40% of homology-based predictions at the 5' end. CONCLUSIONS: De novo comparative gene prediction followed by experimental verification is effective at enhancing the annotation of the newly sequenced genomes provided by standard homology-based methods.

Anopheles darlingi bionomics and transmission of Plasmodium falciparum, Plasmodium vivax and Plasmodium malariae in Amerindian villages of the Upper-Maroni Amazonian forest, French Guiana

French Guiana is one of the areas in South America most affected by malaria and where the disease has become a serious public health problem. In spite of this situation, little recent entomological data are available from the main localities where the disease occurs, even though they are crucial for development of an effective vector control strategy. A longitudinal entomological survey was carried out from March 2000-February 2002 in three Amerindian villages, namely Twenké, Taluène and Cayodé, located in the Amazonian forest of the Upper-Maroni area, to assess anopheline mosquitoes and malaria transmission dynamics. Anopheles darlingi (Diptera: Culicidae) was the most abundant mosquito species caught during the study. This efficient American malaria vector was active the entire year, but showed an evident peak of abundance during the main rainfall season, from April-June, with an average human biting rate of 255.5 bites per person per night. Parity rates were homogeneous all year, indicating no significant seasonal variability in female survival rates. Estimated vectorial capacity indices were higher during the rainy season, even though the risk of transmission was present throughout the year (VCI > 1). A total of 14 An. darlingi were found infected with Plasmodium falciparum, Plasmodium vivax or Plasmodium malariae. The annual circumsporozoite indices were 0.15, 0.14 and 0.05, and the entomological inoculation rates were 22.8, 27.4 and 14.4 infected bites per person per year in Twenké, Taluène and Cayodé, respectively. An. darlingiwas endo-exophagic and rather exophilic in these localities. The species was collected throughout the night but was more aggressive between 21:30-03:30 h and after 05:30 h. Parity rates were homogeneous during the entire night. Impregnated hammock and/or bed nets, coupled with the use of mosquito repellents, as well as the early treatment of malarial cases, appear to be the most suitable tools for fighting malaria in these Amerindian villages since the spraying of residual insecticides is inefficient because of vector biology and the housing structure.

Container productivity, daily survival rates and dispersal of Aedes aegypti mosquitoes in a high income dengue epidemic neighbourhood of Rio de Janeiro: presumed influence of differential urban structure on mosquito biology

Different urban structures might affect the life history parameters of Aedes aegypti and, consequently, dengue transmission. Container productivity, probability of daily survival (PDS) and dispersal rates were estimated for mosquito populations in a high income neighbourhood of Rio de Janeiro. Results were contrasted with those previously found in a suburban district, as well as those recorded in a slum. After inspecting 1,041 premises, domestic drains and discarded plastic pots were identified as the most productive containers, collectively holding up to 80% of the total pupae. In addition, three cohorts of dust-marked Ae. aegypti females were released and recaptured daily using BGS-Traps, sticky ovitraps and backpack aspirators in 50 randomly selected houses; recapture rate ranged from 5-12.2% within cohorts. PDS was determined by two models and ranged from 0.607-0.704 (exponential model) and 0.659-0.721 (non-linear model), respectively. Mean distance travelled varied from 57-122 m, with a maximum dispersal of 263 m. Overall, lower infestation indexes and adult female survival were observed in the high income neighbourhood, suggesting a lower dengue transmission risk in comparison to the suburban area and the slum. Since results show that urban structure can influence mosquito biology, specific control strategies might be used in order to achieve cost-effective Ae. aegypti control.

Biology, diversity and strategies for the monitoring and control of triatomines - Chagas disease vectors

Despite the relevant achievements in the control of the main Chagas disease vectors Triatoma infestans and Rhodnius prolixus, several factors still promote the risk of infection. The disease is a real threat to the poor rural regions of several countries in Latin America. The current situation in Brazil requires renewed attention due to its high diversity of triatomine species and to the rapid and drastic environmental changes that are occurring. Using the biology, behaviour and diversity of triatomines as a basis for new strategies for monitoring and controlling the vectorial transmission are discussed here. The importance of ongoing long-term monitoring activities for house infestations by T. infestans, Triatoma brasiliensis, Panstrongylus megistus, Triatoma rubrovaria and R. prolixus is also stressed, as well as understanding the invasion by sylvatic species. Moreover, the insecticide resistance is analysed. Strong efforts to sustain and improve surveillance procedures are crucial, especially when the vectorial transmission is considered interrupted in many endemic areas.

CoDa-dendrogram: A new exploratory too

The use of orthonormal coordinates in the simplex and, particularly, balance coordinates, has suggested the use of a dendrogram for the exploratory analysis of compositional data. The dendrogram is based on a sequential binary partition of a compositional vector into groups of parts. At each step of a partition, one group of parts isdivided into two new groups, and a balancing axis in the simplex between both groupsis defined. The set of balancing axes constitutes an orthonormal basis, and the projections of the sample on them are orthogonal coordinates. They can be represented in adendrogram-like graph showing: (a) the way of grouping parts of the compositional vector; (b) the explanatory role of each subcomposition generated in the partition process;(c) the decomposition of the total variance into balance components associated witheach binary partition; (d) a box-plot of each balance. This representation is useful tohelp the interpretation of balance coordinates; to identify which are the most explanatory coordinates; and to describe the whole sample in a single diagram independentlyof the number of parts of the sample

Genetic-morphometric variation in Culex quinquefasciatus from Brazil and La Plata, Argentina

Variation among natural populations of Culex (Culex) quinquefasciatus Say is associated with different vectorial capacities. The species Cx. quinquefasciatus is present in the equatorial, tropical and subtropical zones in the Brazilian territory, with intermediate forms between Cx. quinquefasciatus and Culex pipiens occurring in regions of latitudes around 33°-35°S. Herein, we studied geographically distinct populations of Cx. quinquefasciatus by genetic characterization and analysis of intra-specific wing morphometrics. After morphological analysis, molecular characterization of Cx. quinquefasciatus and intermediate forms was performed by polymerase chain reaction of the polymorphic nuclear region of the second intron of the acetylcholinesterase locus. Additionally, the morphology of adult female wings collected from six locations was analyzed. Wing centroid sizes were significantly different between some geographical pairs. Mean values of R2/R2+3 differed significantly after pairwise comparisons. The overall wing shape represented by morphometric characters could be divided into two main groupings. Our data suggest that Brazilian samples are morphologically and genetically distinct from the Argentinean samples and also indicated a morphological distinction between northern and southern populations of Brazilian Cx. quinquefasciatus. We suggest that wing morphology may be used for preliminary assessment of population structure of Cx. quinquefasciatusin Brazil.

Compositional evolution with mass transfer in closed systems

Evolution of compositions in time, space, temperature or other covariates is frequentin practice. For instance, the radioactive decomposition of a sample changes its composition with time. Some of the involved isotopes decompose into other isotopes of thesample, thus producing a transfer of mass from some components to other ones, butpreserving the total mass present in the system. This evolution is traditionally modelledas a system of ordinary di erential equations of the mass of each component. However,this kind of evolution can be decomposed into a compositional change, expressed interms of simplicial derivatives, and a mass evolution (constant in this example). A rst result is that the simplicial system of di erential equations is non-linear, despiteof some subcompositions behaving linearly.The goal is to study the characteristics of such simplicial systems of di erential equa-tions such as linearity and stability. This is performed extracting the compositional differential equations from the mass equations. Then, simplicial derivatives are expressedin coordinates of the simplex, thus reducing the problem to the standard theory ofsystems of di erential equations, including stability. The characterisation of stabilityof these non-linear systems relays on the linearisation of the system of di erential equations at the stationary point, if any. The eigenvelues of the linearised matrix and theassociated behaviour of the orbits are the main tools. For a three component system,these orbits can be plotted both in coordinates of the simplex or in a ternary diagram.A characterisation of processes with transfer of mass in closed systems in terms of stability is thus concluded. Two examples are presented for illustration, one of them is aradioactive decay

Distribution and infection of triatomines (Hemiptera: Reduviidae) by Trypanosoma cruzi in the state of Michoacán, Mexico

An entomological study of triatomine species was carried out to assess their prevalence in 10 localities of the state of Michoacán, Mexico. Entomological indices were calculated to estimate the risk for vector-borne transmission of Trypanosoma cruzi to the human population in this area. Four triatomine species (Triatoma barberi, Triatoma dimidiata, Meccus pallidipennis and Meccus longipennis) were collected from the study area. This is the first report of M. longipennis and T. dimidiata in Michoacán. M. pallidipennis was significantly (p < 0.05) more abundant than any of the other species collected in the study area. Infection indices were greater than 50% for each of the four collected triatomine species. Significantly more triatomines were collected from intradomiciliary areas than from peridomiciliary or sylvatic areas. Infestation, crowding and density indices were low, whereas colonisation indices were high in five localities. The current vectorial conditions in the study area require continuous entomological and serological surveillance to diminish the risk of T. cruzi transmission to human populations.

Morphological and morphometrical assessment of spermathecae of Aedes aegypti females

The vectorial capacity of Aedes aegypti is directly influenced by its high reproductive output. Nevertheless, females are restricted to a single mating event, sufficient to acquire enough sperm to fertilize a lifetime supply of eggs. How Ae. aegypti is able to maintain viable spermatozoa remains a mystery. Male spermatozoa are stored within either of two spermathecae that in Ae. aegypti consist of one large and two smaller organs each. In addition, each organ is divided into reservoir, duct and glandular portions. Many aspects of the morphology of the spermatheca in virgin and inseminated Ae. aegypti were investigated here using a combination of light, confocal, electron and scanning microscopes, as well as histochemistry. The abundance of mitochondria and microvilli in spermathecal gland cells is suggestive of a secretory role and results obtained from periodic acid Schiff assays of cell apexes and lumens indicate that gland cells produce and secrete neutral polysaccharides probably related to maintenance of spermatozoa. These new data contribute to our understanding of gamete maintenance in the spermathecae of Ae. aegypti and to an improved general understanding of mosquito reproductive biology.

A genome-wide association search for type 2 diabetes genes in African Americans.

African Americans are disproportionately affected by type 2 diabetes (T2DM) yet few studies have examined T2DM using genome-wide association approaches in this ethnicity. The aim of this study was to identify genes associated with T2DM in the African American population. We performed a Genome Wide Association Study (GWAS) using the Affymetrix 6.0 array in 965 African-American cases with T2DM and end-stage renal disease (T2DM-ESRD) and 1029 population-based controls. The most significant SNPs (n = 550 independent loci) were genotyped in a replication cohort and 122 SNPs (n = 98 independent loci) were further tested through genotyping three additional validation cohorts followed by meta-analysis in all five cohorts totaling 3,132 cases and 3,317 controls. Twelve SNPs had evidence of association in the GWAS (P<0.0071), were directionally consistent in the Replication cohort and were associated with T2DM in subjects without nephropathy (P<0.05). Meta-analysis in all cases and controls revealed a single SNP reaching genome-wide significance (P<2.5×10(-8)). SNP rs7560163 (P = 7.0×10(-9), OR (95% CI) = 0.75 (0.67-0.84)) is located intergenically between RND3 and RBM43. Four additional loci (rs7542900, rs4659485, rs2722769 and rs7107217) were associated with T2DM (P<0.05) and reached more nominal levels of significance (P<2.5×10(-5)) in the overall analysis and may represent novel loci that contribute to T2DM. We have identified novel T2DM-susceptibility variants in the African-American population. Notably, T2DM risk was associated with the major allele and implies an interesting genetic architecture in this population. These results suggest that multiple loci underlie T2DM susceptibility in the African-American population and that these loci are distinct from those identified in other ethnic populations.

Phlebotomine fauna, natural infection rate and feeding habits of Lutzomyia cruzi in Jaciara, state of Mato Grosso, Brazil

Visceral leishmaniasis (VL) in Brazil is transmitted by the phlebotomine Lutzomyia longipalpis and in some midwestern regions by Lutzomyia cruzi. Studies of the phlebotomine fauna, feeding habits and natural infection rate by Leishmania contribute to increased understanding of the epidemiological chain of leishmaniases and their vectorial capacity. Collections were performed in Jaciara, state of Mato Grosso from 2010-2013, during which time 2,011 phlebotomines (23 species) were captured (68.70% Lu. cruzi and 20.52% Lutzomyia whitmani). Lu. cruzi females were identified by observing the shapes of the cibarium (a portion of the mouthpart) and spermatheca, from which samples were obtained for polymerase chain reaction to determine the rates of natural infection. Engorged phlebotomines were assessed to identify the blood-meal host by ELISA. A moderate correlation was discovered between the number of Lu. cruzi and the temperature and the minimum rate of infection was 6.10%. Twenty-two females were reactive to the antisera of bird (28%), dog (3.30%) and skunk (1.60%). We conclude that Lu. cruzi and Lu. whitmani have adapted to the urban environment in this region and that Lu. cruzi is the most likely vector of VL in Jaciara. Moreover, maintenance of Leishmania in the environment is likely aided by the presence of birds and domestic and synanthropic animals.

A Factor analysis of hidrochemical composition of Llobregat river basin

Hydrogeological research usually includes some statistical studies devised to elucidate mean background state, characterise relationships among different hydrochemical parameters, and show the influence of human activities. These goals are achieved either by means of a statistical approach or by mixing modelsbetween end-members. Compositional data analysis has proved to be effective with the first approach, but there is no commonly accepted solution to the end-member problem in a compositional framework.We present here a possible solution based on factor analysis of compositions illustrated with a case study.We find two factors on the compositional bi-plot fitting two non-centered orthogonal axes to the most representative variables. Each one of these axes defines a subcomposition, grouping those variables thatlay nearest to it. With each subcomposition a log-contrast is computed and rewritten as an equilibrium equation. These two factors can be interpreted as the isometric log-ratio coordinates (ilr) of three hiddencomponents, that can be plotted in a ternary diagram. These hidden components might be interpreted as end-members.We have analysed 14 molarities in 31 sampling stations all along the Llobregat River and its tributaries, with a monthly measure during two years. We have obtained a bi-plot with a 57% of explained totalvariance, from which we have extracted two factors: factor G, reflecting geological background enhanced by potash mining; and factor A, essentially controlled by urban and/or farming wastewater. Graphicalrepresentation of these two factors allows us to identify three extreme samples, corresponding to pristine waters, potash mining influence and urban sewage influence. To confirm this, we have available analysisof diffused and widespread point sources identified in the area: springs, potash mining lixiviates, sewage, and fertilisers. Each one of these sources shows a clear link with one of the extreme samples, exceptfertilisers due to the heterogeneity of their composition.This approach is a useful tool to distinguish end-members, and characterise them, an issue generally difficult to solve. It is worth note that the end-member composition cannot be fully estimated but only characterised through log-ratio relationships among components. Moreover, the influence of each endmember in a given sample must be evaluated in relative terms of the other samples. These limitations areintrinsic to the relative nature of compositional data

Avalanche dynamics of fiber bundle models

We present a detailed analytical and numerical study of the avalanche distributions of the continuous damage fiber bundle model CDFBM . Linearly elastic fibers undergo a series of partial failure events which give rise to a gradual degradation of their stiffness. We show that the model reproduces a wide range of mechanical behaviors. We find that macroscopic hardening and plastic responses are characterized by avalanche distributions, which exhibit an algebraic decay with exponents between 5/2 and 2 different from those observed in mean-field fiber bundle models. We also derive analytically the phase diagram of a family of CDFBM which covers a large variety of potential avalanche size distributions. Our results provide a unified view of the statistics of breaking avalanches in fiber bundle models

El reto del paisaje urbano en China, del Mall Comercial al espacio público

Las categorías del espacio introvertido y extrovertido definen por excelencia la estructura espacial, que ordena el ámbito de lo privado y lo público en la ciudad. La dualidad del espacio abierto y cerrado, vinculado a la estructura espacial de la ciudad clásica China, quedaba ordenado, justificado y vinculado mediante una estructura espacial muy definida. Sin embargo en el modelo de ciudad contemporánea, aflora la cuestión de la integración de estas categorías espaciales y su articulación dentro de una estructura urbana heterogénea y fuertemente alterada. ¿Cuáles serán los factores de cambio de la transición de un espacio comunitario introvertido a un espacio cívico abierto? Este proceso es un proceso que debe discurrir a un doble nivel espacial y político. Debe discurrir en paralelo a la transición de las categorías espaciales que ordenan identitariamente el ámbito urbano y la progresiva transición socio-cultural y política de una sociedad que debe gradualmente identificar y adoptar como propias las instituciones de gobierno local y su escenario, la ciudad.

Gene finding in the chicken genome

Background: Despite the continuous production of genome sequence for a number of organisms,reliable, comprehensive, and cost effective gene prediction remains problematic. This is particularlytrue for genomes for which there is not a large collection of known gene sequences, such as therecently published chicken genome. We used the chicken sequence to test comparative andhomology-based gene-finding methods followed by experimental validation as an effective genomeannotation method.Results: We performed experimental evaluation by RT-PCR of three different computational genefinders, Ensembl, SGP2 and TWINSCAN, applied to the chicken genome. A Venn diagram wascomputed and each component of it was evaluated. The results showed that de novo comparativemethods can identify up to about 700 chicken genes with no previous evidence of expression, andcan correctly extend about 40% of homology-based predictions at the 5' end.Conclusions: De novo comparative gene prediction followed by experimental verification iseffective at enhancing the annotation of the newly sequenced genomes provided by standardhomology-based methods.