Assessment of transcript reconstruction methods for RNA-seq.

We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete transcript components with high success rates but that assembly of complete isoform structures poses a major challenge even when all constituent elements are identified. Expression-level estimates also varied widely across methods, even when based on similar transcript models. Consequently, the complexity of higher eukaryotic genomes imposes severe limitations on transcript recall and splice product discrimination that are likely to remain limiting factors for the analysis of current-generation RNA-seq data.

Multilayered genetic and omics dissection of mitochondrial activity in a mouse reference population

The manner by which genotype and environment affect complex phenotypes is one of the fundamental questions in biology. In this study, we quantified the transcriptome--a subset of the metabolome--and, using targeted proteomics, quantified a subset of the liver proteome from 40 strains of the BXD mouse genetic reference population on two diverse diets. We discovered dozens of transcript, protein, and metabolite QTLs, several of which linked to metabolic phenotypes. Most prominently, Dhtkd1 was identified as a primary regulator of 2-aminoadipate, explaining variance in fasted glucose and diabetes status in both mice and humans. These integrated molecular profiles also allowed further characterization of complex pathways, particularly the mitochondrial unfolded protein response (UPR(mt)). UPR(mt) shows strikingly variant responses at the transcript and protein level that are remarkably conserved among C. elegans, mice, and humans. Overall, these examples demonstrate the value of an integrated multilayered omics approach to characterize complex metabolic phenotypes.

Pollicipes caboverdensis sp. nov. (Crustacea: Cirripedia: Scalpelliformes), an intertidal barnacle from the Cape Verde Islands

Recently, genetic evidence supported the existence of a new species of the genus Pollicipes from the Cape Verde Islands, previously considered a population of P. pollicipes. However, P. pollicipes was not sampled at its southern limit of distribution (Dakar, Senegal), which is geographically separated from the Cape Verde Islands by about 500 km. Herein we describe Pollicipes caboverdensis sp. nov. from the Cape Verde Islands and compare its morphology with the other three species of Pollicipes: P. pollicipes, P. elegans and P. polymerus. Pollicipes pollicipes was sampled at both the middle (Portugal) and southern limit (Dakar, Senegal) of its geographical distribution. The genetic divergence among and within these two regions and Cape Verde was calculated through the analysis of partial mtDNA CO1 gene sequences. Pollicipes caboverdensis sp. nov. has a single whorl of capitular plates below the subrostrum, peduncular scales pointing up toward the capitulum and multi-articulate caudal appendages (all characters shared with P. pollicipesand P. elegans), reddish-orange capitular plates (large specimens), a single rostral median latus between the median latus and the rostrolatus (both characters shared with P. elegans), and uniquely possesses peduncular scales that are approximately the same width as height. The genetic distance between the Cape Verde population and the Senegal and Portugal populations is 13–14%, whilst between Senegal and Portugal it is < 1%.

An external site controls closing of the epithelial Na+ channel ENaC.

Members of the ENaC/degenerin family of ion channels include the epithelial sodium channel (ENaC), acid-sensing ion channels (ASICs) and the nematode Caenorhabditis elegans degenerins. These channels are activated by a variety of stimuli such as ligands (ASICs) and mechanical forces (degenerins), or otherwise are constitutively active (ENaC). Despite their functional heterogeneity, these channels might share common basic mechanisms for gating. Mutations of a conserved residue in the extracellular loop, namely the 'degenerin site' activate all members of the ENaC/degenerin family. Chemical modification of a cysteine introduced in the degenerin site of rat ENaC (betaS518C) by the sulfhydryl reagents MTSET or MTSEA, results in a approximately 3-fold increase in the open probability. This effect is due to an 8-fold shortening of channel closed times and an increase in the number of long openings. In contrast to the intracellular gating domain in the N-terminus which is critical for channel opening, the intact extracellular degenerin site is necessary for normal channel closing, as illustrated by our observation that modification of betaS518C destabilises the channel closed state. The modification by the sulfhydryl reagents is state- and size-dependent consistent with a conformational change of the degenerin site during channel opening and closing. We propose that the intracellular and extracellular modulatory sites act on a common channel gate and control the activity of ENaC at the cell surface.

O gênero Xylocopa Latreille no Rio Grande do Sul, Brasil (Hymenoptera, Anthophoridae)

The genus Xylocopa Latreille in Rio Grande do Sul, Brazil (Hymenoptera, Anthophoridae). A survey of the genus Xylocopa Latreille, 1802 is given for Rio Grande do Sul, the southernmost State of Brazil. Data are based on several studies on the bee fauna of southern Brazil and on unpublished observations. A key is provided to the species (males and females) and information on distribution, nesting habits and relation to flowers. Rio Grande do Sul is strikingly rich in species of Xylocopa because of the diversity of habitats and its geographic position in the transition of tropical/subtropical to temperate climate. Nineteen species, classified into ten subgenera, have been recorded in Rio Grande do Sul. Here we maintain the subgenera Ioxylocopa, Megaxylocopa and Xylocospila, which were put into synonymy recently by Minckley (1998). The species are: Xylocopa (Dasyxylocopa) bimaculata Friese, 1903; Xylocopa (Ioxylocopa) chrysopoda Schrottky, 1902; Xylocopa (Megaxylocopa) frontalis (Olivier, 1789); Xylocopa (Nanoxylocopa) ciliata Burmeister, 1876; Xylocopa (Neoxylocopa) augusti Lepeletier, 1841; Xylocopa (N.) brasilianorum (Linnaeus, 1767); Xylocopa (N.) haematospila Moure, 1951; Xylocopa (N.) hirsutissima Maidl, 1912; Xylocopa (N.) nigrocincta Smith, 1854; Xylocopa (N.) ordinaria Smith, 1874; Xylocopa (N.) suspecta Moure & Camargo, 1988; Xylocopa (N.) tacanensis Moure, 1949; Xylocopa (Schonnherria) macrops Lepeletier, 1841; Xylocopa (S.) simillima Smith, 1854; Xylocopa (S.) splendidula Lepeletier, 1841; Xylocopa (S.) varians Smith, 1874; Xylocopa (Stenoxylocopa) artifex Smith, 1874; Xylocopa (Xylocopoda) elegans Hurd & Moure, 1963; Xylocopa (Xylocopsis) funesta Maidl, 1912; Xylocopa (Xylocospila) bambusae Schrottky, 1902. Xylocopa tacanensis is for the first time recorded in Brasil.

Fauna de Dissomphalus Ashmead (Hymenoptera, Bethylidae) da Mata Atlântica Brasileira, com descrição de 23 espécies novas

Foram realizadas coletas padronizadas em 18 pontos ao longo da Mata Atlântica Brasileira no escopo do Programa BIOTA/FAPESP usando-se varredura de vegetação, e armadilhas Malaise e Möricke. Foi coletado um total de 2.811 exemplares de Dissomphalus. Foram reconhecidas 30 espécies descritas, a saber: Dissomphalus conicus Azevedo, 2003, D. h-ramus Redighieri & Azevedo, 2004, D. laminaris Redighieri & Azevedo, 2004, D. manus Azevedo, 2003, D. umbilicus Azevedo, 2003, D. verrucosus Redighieri & Azevedo, 2004, D. alticlypeatus Azevedo, 2003, D. bicerutus Azevedo, 2003, D. gilvipes Evans, 1979, D. krombeini Azevedo, 1999, D. gordus Azevedo, 2003, D. undatus Azevedo, 2003, D. cristatus Redighieri & Azevedo, 2004, D. laticephalus Azevedo, 2003, D. lobicephalus Azevedo, 2003, D. completus Azevedo, 1999, D. gigantus Azevedo, 1999, D. scamatus Azevedo, 1999, D. napo Evans, 1979, D. punctatus (Kieffer, 1910), D. infissus Evans, 1969, D. plaumanni Evans, 1964, D. concavatus Azevedo, 1999, D. rectilineus Azevedo, 1999, D. bifurcatus Azevedo, 1999, D. extrarramis Azevedo, 1999, D. strictus Azevedo, 1999, D. connubialis Evans, 1966, D. microstictus Evans, 1969, D. scopatus Redighieri & Azevedo, 2004. Além disso, foram descritas e ilustradas 23 espécies novas: Dissomphalus inclinatus sp. nov., D. divisus sp. nov., D. distans sp. nov., D. crassus sp. nov., D. filiformis sp. nov., D. inflexus sp. nov., D. spissus sp. nov., D. firmus sp. nov., D. setosus sp. nov., D. tubulatus sp. nov., D. differens sp. nov., D. lamellatus sp. nov., D. fimbriatus sp. nov., D. magnus sp. nov., D. trilobatus sp. nov., D. amplifoveatus sp. nov., D. personatus sp. nov., D. excellens sp. nov., D. peculiaris sp. nov., D. bahiensis sp. nov., D. amplexus sp. nov., D. elegans sp. nov. e D. amplus sp. nov.. Foram propostos 2 grupos novos de espécies, brasiliensis com duas espécies e setosus com oito espécies. Dissomphalus connubialis Evans, 1966 foi revalidado a partir de D. brasiliensis Kieffer, 1910. Dissomphalus bispinulatus Evans, 1969 foi considerado sinônimo junior de D. brasiliensis. Foi proposto para o gênero uma chave de espécies Neotropicais baseada em machos. Algumas espécies como Dissomphalus rectilineus, D. plaumanni, D. connubialis e D. gigantus são amplamente distribuídos ao longo deste bioma. Por outro lado, espécies como Dissomphalus completus, D. bifurcatus, D. napo, D. gilvipes, D. microstictus, D. brasiliensis, D. scamatus, D. strictus, D. undatus, D. alticlypeatus, D. laticephalus, D. verrucosus, D. extrarramis, D. concavatus, D. krombeini, D. gordus, D. lobicephalus e 13 espécies novas são restritas a regiões específicas, apresentando congruência com os subcentros deste bioma.

Revisão taxonômica, análise cladística e descrição de espécies novas de Aglaenita Spinola (Hemiptera, Cicadellidae, Neocoelidiinae)

Aglaenita e as quatro espécies conhecidas do gênero são redescritas. Nove espécies novas são descritas. Foi realizada uma análise cladística baseada em 22 caracteres morfológicos e 15 táxons terminais, utilizando duas espécies de Biza como grupo externo. A análise mostrou que Aglaenita é um gênero monofilético e o relacionamento entre as espécies foi: (A. spatulata sp. nov. ((A. dubia, A. elegans) ((A. bicornis sp. nov., A. spinipenis sp. nov.) (A. bifurcata sp. nov. (A. affinis sp. nov. ((A. bipunctata (A. similis, A. tridentata sp. nov.)) (A. longicornis sp. nov. (A. coariensis sp. nov., A. unciformis sp. nov.)))))))). As treze espécies são ilustradas, uma chave para identificação das mesmas e sua distribuição geográfica conhecida são fornecidas. A fêmea de A. elegans é descrita pela primeira vez.

A propos de la position systématique des genres Nectogale et Chimarrogale (Mammalia, Insectivora)

The terminal segment of the intermediate hair in the semi-aquatic Chirmarrogale hantu and Bectigale elegans is investigated with a view to a taxonomic interpretation. Nectogale is characterized by especially fine hairs which strongly contrast with the distally thickened hairs of Chimarrogale. In spite of these differences, the hairs of both genera are characterized by a H-shaped profile. According to Vogel & Köpchen (1977), this criterion confirms the discussed membership to the Soricinae.

Novo gênero e espécie de Portanini Linnavuori, e notas taxonômicas (Hemiptera, Cicadellidae, Xestocephalinae)

Nove espécies são transferidas de Portanus Ball, 1932 para Paraportanus gen. nov.: Paraportanus longicornis (Osborn, 1923) comb. nov. = Portanus chelatus DeLong, 1976 syn. nov.; Paraportanus elegans (Kramer, 1961) comb. nov.; Paraportanus facetus (Kramer, 1961) comb. nov.; Paraportanus eburatus (Kamer, 1964) comb. nov.; Paraportanus filamentus (DeLong, 1980) comb. nov.; Paraportanus bicornis (Carvalho & Cavichioli, 2003) comb. nov.; Paraportanus bimaculatus (Carvalho & Cavichioli, 2003) comb. nov.; Paraportanus cinctus (Carvalho & Cavichioli, 2003) comb. nov.; Paraportanus variatus (Carvalho & Cavichioli, 2003) comb. nov.. Novos dados de distribuição geográfica são registrados para: P. facetus; P. elegans e P. longicornis. Chave para identificação das espécies é apresentada.

Three new species and synonymy in Nealcidion Monné (Coleoptera, Cerambycidae, Lamiinae)

Three new species of Nealcidion Monné are described: N. antennatum Monné & Monné sp. nov. from Panamá and N. albolineatum Monné & Monné sp. nov. and N. elegans Monné & Monné sp. nov., from Venezuela. Alcidion deletum Bates, 1880 is considered a synonym of Nealcidion strigilis (Erichson, 1847) comb. nov. The four species are illustrated.

Características de la vida planctónica y colonización de los organismos betónicos epilíticos durante el fenómeno El Niño

Durante «El Niño» (EN) de 1982 - 1983 se realizaron 2 experimentos en la Bahía de Ancón, a fin de reconocer las principales características de la reco­lonización en la biocenosis de Semimytilus algosus (zona mediolitoral), utilizando áreas cuadradas denudadas de 0,0625 m2 ; y en la de Aulacomya ater (a 5 metros de profundidad), colocando prismas triangulares de 0,2 m2 de área junto a un pequeño banco de este mitílido. Se analizaron periódicamente los cambios en el número de especies, densidad, biomasa, diversidad y velocidad de crecimiento de los principales coloniza­ dores. Paralelamente se tomaron datos oceanográficos y muestras periódicas de zooplancton y fitoplancton. En medio año de colonización, las características estructurales y tróficas de las 2 comunidades en suce­ sión han seguido patrones distintos, pero con un evidente proceso de tropicalización en ambos casos. Las larvas planctónicas con mayor abundancia a lo largo de todo el año pertenecieron al braquiópodo Discinisca lamellosa, a cirrípedos, gasterópodos y pelecípodos. En los experimentos, los mejores colonizadores primarios resultaron : Viva costata y Semimytilus algosus, en los cuadrados ; Hydroides parvus e Hydroides norvegica, en los prismas. Los mecanismos de competencia fueron más importantes en los cuadrados, destacando la ejercida por especies foráneas de aguas cálidas ( Pollicipes elegans, Pomatoceros sp.). En los prismas destacan los mecanismos de predación y resalta también la colonización por especies de aguas cálidas (Pomatoceros sp., Pteria sterna ) y por especies tradicionalmente escasas en la bahía (Argopecten purpuratus).

Efectos del Fenómeno «El Niño» sobre el Fitoplancton

El fenómeno «El Niño» (EN) que se caracteriza por la presencia de aguas de altas temperaturas y salinidades mayores de 35%0 o menos de 34,8%0 , de acuerdo a la masa de agua que ingresa, produce cambios significativos en la comunidad fitoplanctónica tanto en la abundancia, distribución, así como en la composición específica. La biomasa planctónica en la costa peruana normal­ mente es alta, presentando volúmenes promedios ma­ yores de 3 mi m -3, pero cuando se producen alteraciones como el fenómeno EN encontramos los volúmenes promedio bajos, menores que 1 mi m -3 . En cuanto a la distribución, el fitoplancton en épocas normales está constituido principalmente por las diatomeas, las mismas que se distribuyen a lo largo de la costa y en su mayoría hasta las 60 millas, afuera de ella el fitoplancton está representado por los dinotlagela­ dos; mientras que, en épocas consideradas como EN las diatomeas se distribuyen dentro de las 10 millas y los dinotlagelados propios de aguas calientes se acercan generalmente hasta las 10 millas de la costa. La composición del fitoplancton también varía. En años considerados normales la predominancia está dada por diatomeas como : Schroderella delicatula, Thalassionema nitzschioides, Skeletonema costatum, Asterionella japonica y Chaetoceros y los dinotlagela­ dos: Ceratiumfurca, Protoperidinium obtusum, etc. En épocas consideradas anormales se presentan otras especies como : Thalassiosira partheneia, Rhizosolenia temperei, Rh. castracanei, Streptotheca thamensis y Biddulphia sinensis ; dentro de los dinotlagelados : Cera­ tium breve, C. extensum, C. longirostrum, C. trichoceros, Ceratocorys horrida, Ornithocercus magnificus, O. qua­ dratus, O. steinii y Protoperidinium elegans.

Veliidae (Insecta, Heteroptera, Gerromorpha) from southeastern Brazil: three new species from Rio de Janeiro State, a new species group for Neotropical Rhagovelia Mayr, and notes on distribution and synonymy

Microvelia nelsoni sp. nov., M. takiyae sp. nov., and Rhagovelia mangaratiba sp. nov. are described. Rhagovelia scitula and R. whitei are transferred from the robusta group to the new whitei group. Rhagovelia denticulata is synonymized under R. scitula. Microvelia longipes, Oiovelia brasiliensis, Rhagovelia sooretama, R. trianguloides, R. vaniniae, and Stridulivelia quadrispinosa are recorded for the first time from Rio de Janeiro State. Additional new municipality records in Rio de Janeiro State are presented for Microvelia braziliensis, M. ioana, M. mimula, M. pulchella, Paravelia basalis, P. itatiayana, Rhagovelia accedens, R. agra, R. aiuruoca, R. elegans, R. hambletoni, R. henryi, R. itatiaiana, R. lucida, R. macta, R. modesta, R. novana, R. scitula, R. tenuipes, R. tijuca, R. triangula, and R. zela. Corrections are presented for the previously published distributions of Rhagovelia aiuruoca, R. lucida, R. macta, and R. triangula.

Isla Lobos de Tierra: Evaluación de invertebrados en bancos naturales, 2010

Las tallas de Transennella pannosa fluctuaron entre 10 y 34 mm de altura valvar, con media en 27,2 mm; predominaron ejemplares maduros (55,56%) y en evacuación (27,78%); se distribuyó entre 6°25’46,6’’S y 6°27’24,8’’S, en concentraciones de 4478 ind.m-2, la biomasa estimada fue 1566,7 t y la población 248,4 millones de ejemplares. La talla de Pollicipes elegans varió entre 6 y 40 mm de longitud carina rostral, media 26,2 mm; los juveniles (Lcr<17 mm) fueron el 11,63% y los adultos (Lcr≥17 mm) el 88,37%; predominaron ejemplares maduros (72,09%). La talla de Argopecten purpuratus varió entre 9 y 82 mm de altura valvar, media de 56,7 mm; los juveniles (<25 mm) fueron el 0,41% y los adultos comerciales (≥65 mm) el 15,27%; predominaron los desovantes (73,62%); se distribuyó entre 6°21’54,8’’S y 6°25’33,6’’S con concentraciones absolutas de 1 a 121 ejem.m-2 en profundidades de 6,2 a 24,9 m. Las tallas de Octopus mimus fluctuaron entre 100 y 200 mm de longitud del manto; en hembras predominó madurez total y post-fresa, ambos con 40%.

Mechanisms of spindle positioning during "Caenorhabditis elgans" asymmetric cell division

Résumé : Le positionnement correct du fuseau mitotique est crucial pour les divisions cellulaires asymétriques, car il gouverne le contrôle spatial de la division cellulaire et assure la ségrégation adéquate des déterminants cellulaires. Malgré leur importance, les mécanismes contrôlant le positionnement du fuseau mitotique sont encore mal compris. Chez l'embryon au stade une-cellule du nématode Caenorhabditis elegans, le fuseau mitotique est positionné de manière asymétrique durant l'anaphase grâce à l'action de générateurs de force situés au cortex cellulaire, et dont la nature était jusqu'alors indéterminée. Ces générateurs de force corticaux exercent une traction sur les microtubules astraux et sont dépendants de deux protéines Gα et de leurs protéines associées. Cette thèse traite de la nature de la machinerie responsable pour la génération des forces de tractions, ainsi que de son lien avec les protéines Gα et associées. Nous avons combiné des expériences de coupure par faisceau laser du fuseau mitotique avec le contrôle temporel de l'inactivation de gènes ou de l'exposition à des produits pharmacologiques. De cette manière, nous avons établi que la dynéine, un moteur se déplaçant vers l'extrémité négative des microtubules, ainsi que la dynamique des microtubules, sont toutes deux requises pour la génération efficace des forces de tractions. Nous avons démontré que les protéines Gα et leurs protéines associées GPR-1/2 et LIN-5 interagissent in vivo avec LIS-1, un composant du complexe de la dynéine. De plus, nous avons découvert que les protéines Gα, GPR-1/2 et LIN-5 promeuvent la présence du complexe de la dynéine au cortex cellulaire. Nos résultats suggèrent un mécanisme par lequel les protéines Gα permettent le recrutement cortical de GPR-1/2 et LIN-5, assurant ainsi la présence de la dynéine au cortex. Conjointement avec la dynamique des microtubules, ce mécanisme permet la génération des forces de tractions afin d'obtenir une division cellulaire correcte. Comme les mécanismes contrôlant le positionnement du fuseau mitotique et les divisions cellulaires asymétriques sont conservés au cours de l'évolution, nous espérons que les mécanismes élucidés par ce travail sont d'importance générale pour la génération de la diversité cellulaire durant le développement. De plus, ces mécanismes pourraient être applicables à d'autres divisions asymétriques, comme celle des cellules souches, dont le disfonctionnement peut entraîner la génération de cellules cancéreuses. Abstract : Proper spindle positioning is crucial for asymmetric cell division, because it controls spatial aspects of cell division and the correct inheritance of cell-fate determinants. However, the mechanisms governing spindle positioning remain incompletely understood. In the Caenorhabditis elegans one-cell stage embryo, the spindle becomes asymmetrically positioned during anaphase through the action of as-yet unidentified cortical force generators that pull on astral microtubules and that depend on two Gα proteins and associated proteins. This thesis addresses the nature of the force generation machinery and the link with the Gα and associated proteins. By performing spindle-severing experiments following temporally restricted gene inactivation and drug exposure, we established that microtubule dynamics and the minus-end directed motor dynein are both required for generating efficient pulling forces. We discovered that the Gα proteins and their associated proteins GPR-1/2 and LIN-5 interact in vivo with LIS-1, a component of the dynein complex. Moreover, we uncovered that LIN-5, GPR-1/2 and the Gα proteins promote the presence of the dynein complex at the cell cortex. Our findings suggest a mechanism by which the Gα proteins enable GPR-1/2 and LIN-5 recruitment to the cortex, thus ensuring the presence of cortical dynein. Together with microtubule dynamics, this allows pulling forces to be exerted and proper cell division to be achieved. Because the mechanisms of spindle positioning and asymmetric cell division are conserved across evolution, we expect the underlying mechanism uncovered here to be of broad significance for the generation of cell diversity during development. Moreover, this mechanism could be relevant for other asymmetric cell divisions, such as stem cell divisions, whose dysfunction may lead to the generation of cancer cells.