Protein identification pipeline for the homology-driven proteomics

Homology-driven proteomics is a major tool to characterize proteomes of organisms with unsequenced genomes. This paper addresses practical aspects of automated homology-driven protein identifications by LC-MS/MS on a hybrid LTQ orbitrap mass spectrometer. All essential software elements supporting the presented pipeline are either hosted at the publicly accessible web server, or are available for free download. (C) 2008 Elsevier B.V. All rights reserved.

Coding behavioural data for cladistic analysis: using dynamic homology without parsimony

Many of the controversies around the concept of homology rest on the subjectivity inherent to primary homology propositions. Dynamic homology partially solves this problem, but there has been up to now scant application of it outside of the molecular domain. This is probably because morphological and behavioural characters are rich in properties, connections and qualities, so that there is less space for conflicting character delimitations. Here we present a new method for the direct optimization of behavioural data, a method that relies on the richness of this database to delimit the characters, and on dynamic procedures to establish character state identity. We use between-species congruence in the data matrix and topological stability to choose the best cladogram. We test the methodology using sequences of predatory behaviour in a group of spiders that evolved the highly modified predatory technique of spitting glue onto prey. The cladogram recovered is fully compatible with previous analyses in the literature, and thus the method seems consistent. Besides the advantage of enhanced objectivity in character proposition, the new procedure allows the use of complex, context-dependent behavioural characters in an evolutionary framework, an important step towards the practical integration of the evolutionary and ecological perspectives on diversity. (C) The Willi Hennig Society 2010.

Metastatic melanoma positively influences pregnancy outcome in a mouse model: could a deadly tumor support embryo life?

The incidence of melanoma is increasing worldwide. It is one of the leading cancers in pregnancy and the most common malignancy to metastasize to placenta and fetus. There are no publications about experimental models of melanoma and pregnancy. We propose a new experimental murine model to study the effects of melanoma on pregnancy and its metastatic process. We tested several doses of melanoma cells until we arrived at the optimal dose, which produced tumor growth and allowed animal survival to the end of pregnancy. Two control groups were used: control (C) and stress control (SC) and three different routes of inoculation: intravenous (IV), intraperitoneal (IP) and subcutaneous (SC). All the fetuses and placentas were examined macroscopically and microscopically. The results suggest that melanoma is a risk factor for intrauterine growth restriction but does not affect placental weight. When inoculated by the SC route, the tumor grew only in the site of implantation. The IP route produced peritoneal tumoral growth and also ovarian and uterine metastases in 60% of the cases. The IV route produced pulmonary tumors. No placental or fetal metastases were obtained, regardless of the inoculation route. The injection of melanoma cells by any route did not increase the rate of fetal resorptions. Surprisingly, animals in the IV groups had no resorptions and a significantly higher number of fetuses. This finding may indicate that tumoral factors released in the host organism to favor tumor survival may also have a pro-gestational action and consequently improve the reproductive performance of these animals.

Exogenous insulin stimulates glycogen accumulation in Rhipicephalus (Boophilus) microplus embryo cell line BME26 via PI3K/AKT pathway

Ticks are obligatory blood-feeding arthropods and important vectors of both human and animal disease agents. Besides its metabolic role, insulin signaling pathway (ISP) is widely described as crucial for vertebrate and invertebrate embryogenesis, development and cell survival. In such cascade, Phosphatidylinositol 3-OH Kinase (PI3K) is hierarchically located upstream Protein Kinase B (PKB). To study the insulin-triggered pathway and its possible roles during embryogenesis we used a culture of embryonic Rhipicephalus microplus cells (BME26). Exogenous insulin elevated cell glycogen content in the absence of fetal calf serum (FCS) when compared to cells without treatment. Moreover, in the presence of PI3K inhibitors (Wortmannin or LY294002) these effects were blocked. We observed an increase in the relative expression level of PI3K`s regulatory subunit (p85), as determined by qRT-PCR. In the presence of PI3K inhibitors these effects on transcription were also reversed. Additionally, treatment with Wortmannin increased the expression level of the insulin-regulated downstream target glycogen synthase kinase 3 beta (GSK3 beta). The p85 subunit showed elevated transcription levels in ovaries from fully engorged females, but was differentially expressed during tick embryogenesis. These results strongly suggest the presence of an insulin responsive machinery in BME26 cells, and its correlation with carbohydrate/glycogen metabolism also during embryogenesis. (C) 2009 Published by Elsevier Inc.

The crystal structure of the leptospiral hypothetical protein LIC12922 reveals homology with the periplasmic chaperone SurA

Leptospirosis is a world spread zoonosis caused by members of the genus Leptospira. Although leptospires were identified as the causal agent of leptospirosis almost 100 years ago, little is known about their biology, which hinders the development of new treatment and prevention strategies. One of the several aspects of the leptospiral biology not yet elucidated is the process by which outer membrane proteins (OMPs) traverse the periplasm and are inserted into the outer membrane. The crystal structure determination of the conserved hypothetical protein LIC12922 from Leptospira interrogans revealed a two domain protein homologous to the Escherichia coli periplasmic chaperone SurA. The LIC12922 NC-domain is structurally related to the chaperone modules of E. coli SurA and trigger factor, whereas the parvulin domain is devoid of peptidyl prolyl cis-trans isomerase activity. Phylogenetic analyses suggest a relationship between LIC12922 and the chaperones PrsA, PpiD and SurA. Based on our structural and evolutionary analyses, we postulate that LIC12922 is a periplasmic chaperone involved in OMPs biogenesis in Leptospira spp. Since LIC12922 homologs were identified in all spirochetal genomes sequenced to date, this assumption may have implications for the OMPs biogenesis studies not only in leptospires but in the entire Phylum Spirochaetes. (C) 2010 Elsevier Inc. All rights reserved.

The first group (co)homology of a group G with coefficients in some G-modules

Let G be a group. We give some formulas for the first group homology and cohomology of a group G with coefficients in an arbitrary G-module (Z) over tilde. More explicit calculations are done in the special cases of free groups, abelian groups and nilpotent groups. We also perform calculations for certain G-module M, by reducing it to the case where the coefficient is a G-module (Z) over tilde. As a result of the well known equalities H-1(X, M) = H-1(pi(1)(X), M) and H-1(X, M) = H-1(pi(1) (X), M), for any G-module M, we are able to calculate the first homology and cohomology groups of topological spaces with certain local system of coefficients.

Morfologia e avaliação do crescimento inicial de plântulas de Bactris gasipaes Kunth. (arecaceae) em diferentes substratos

Este trabalho teve por objetivos descrever a morfologia dos diásporos, as fases da germinação e determinar o substrato mais adequado para o crescimento inicial de plântulas de pupunha. Periodicamente, unidades representativas de cada fase de germinação foram retiradas para a descrição da seqüência dos eventos morfológicos. Os substratos usados para o crescimento inicial foram Plantmax HT, areia, terra (latossolo roxo) e outro com proporções iguais de terra, areia e esterco (TAE). Avaliou-se o crescimento inicial das plântulas aos 101 dias após o transplante, com base na sua altura, número de folhas, comprimento e largura das folhas. Observou-se que as sementes são albuminosas, com endosperma oleaginoso e de consistência relativamente dura. O embrião é lateral, periférico e relativamente indiferenciado, de forma cônica. A germinação inicia-se com o desenvolvimento de uma massa de células indiferenciadas na depressão micropilar. Posteriormente, esta massa de células torna-se cilíndrica, com a diferenciação dos primórdios caulinar e radicular. O primórdio caulinar é constituído por três bainhas envolvendo a primeira folha. Estas se abrem sucessivamente, permitindo a emergência da folha primária. Entre os substratos testados, de acordo com os parâmetros avaliados, os mais adequados para crescimento inicial de mudas de Bactris gasipaes Kunth foram o TAE e o Plantmax.

Aspectos morfológicos, germinação e desenvolvimento inicial de plântulas de Archontophoenix alexandrae (F. Mueller) H. Wendl. e Drude (Arecaceae) em diferentes substratos

Este trabalho teve por objetivo descrever a morfologia dos diásporos e as suas fases de germinação, bem como determinar o substrato mais adequado para a germinação das sementes e o crescimento das plântulas de palmeira-da-rainha (Archontophoenix alexandrae (F. Mueller) H. Wendl. e Drude). Periodicamente, unidades representativas de cada fase de germinação foram retiradas para as descrições morfológicas. Os substratos utilizados foram Plantmax®, areia, terra (latossolo roxo) e outro com proporções iguais de terra, areia e esterco (TAE). Foi instalado um experimento em delineamento inteiramente casualizado. Avaliaram-se a porcentagem, o tempo médio de germinação e o crescimento inicial das plântulas aos 135 dias após a emergência, com base na altura, diâmetro do colo e número, comprimento e largura das folhas. As sementes são albuminosas, com endosperma ruminado e oleaginoso, e o embrião é lateral, periférico e relativamente indiferenciado. A germinação é do tipo criptocotiledonar hipógea, iniciando-se com a formação de uma massa de células indiferenciadas na depressão micropilar. Essa massa de células torna-se cilíndrica, com a diferenciação dos primórdios caulinares e radiculares. Concomitantemente, ocorre o desenvolvimento de raízes adventícias no eixo embrionário. O substrato mais indicado para a germinação de sementes de palmeira-da-rainha é o Plantmax®, porém, para o crescimento inicial, indica-se Plantmax® e TAE.

Morfologia de frutos e sementes de espécies arbóreas do gênero Solanum L.

O objetivo do trabalho foi caracterizar a morfologia do fruto e da semente de três espécies florestais nativas do Brasil, Solanum granuloso-leprosum Dunal, S. lycocarpum A.St.-Hil. e S. pseudoquina A.St.-Hil., recomendadas para plantações destinadas à recuperação de áreas degradadas. Os frutos são indeiscentes, carnosos, do tipo baga, globosos, polispérmicos e constituídos por dois ou mais lóculos. As sementes são estenospérmicas, campilótropas, elipsóides, comprimidas, apresentando seção longitudinal largo-ovalada ou achatado-ovalada e seção transversal elíptica. Hilo mediano-marginal localizado em uma depressão e micrópila arredondada. Sementes albuminosas, com endosperma abundante, periférico, carnoso-firme, semitransparente e de coloração esbranquiçada. Embrião axial, linear, contínuo e curvado. em Solanum lycocarpum e S. pseudoquina o embrião é circinado e em S. granuloso-leprosum é espiralado.

Induction of the acrosome reaction test to in vitro estimate embryo production in Nelore cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The effects of macromolecular and serum supplements and oxygen tension during bovine in vitro procedures on kinetics of oocyte maturation and embryo development

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Effect of breed and corpus luteum on pregnancy rate of bovine embryo recipients

The objective of this study was to evaluate pregnancy rates of recipients of different breed groups (Nellore and crossbreed), as well as the effects of size and type of the corpus luteum (CL) on plasmatic concentrations of progesterone and pregnancy rates of embryo recipients. A total of 152 heifers were synchronized with progesterone implants and on the day of embryo transfer, previously obtained by superovulation and frozen in ethylene glycol, the diameter and type of the corpus luteum (cavitary and compact) was measured and blood was collected for progesterone measurement. The pregnancy rate was 44.1%, with a diameter of corpus luteum higher in recipients that became pregnant (2.03±0.41) compared with non-pregnant ones (1.86±0.34 cm). Plasmatic concentrations of progesterone did not differ between pregnant (1.50±1.05) and non-pregnant (1.31±0.91 ng/mL) animals. The type of corpus luteum did not influence the pregnancy rates. Only Angus and crossbred Marchigiana differ among themselves in pregnancy rates (33.3 and 59.2%, respectively). The pregnancy probability was affected only by CL diameter, but not by P4 plasmatic concentration. Selection of the corpus luteum size at the time of embryo transfer is an important factor to increase pregnancy rates in recipients, and compact and cavitary corpora lutea do not influence the pregnancy rates of bovine embryo recipients. Nellore recipients have pregnancy rates that are satisfactory and comparable to crossbred (Bos taurus × Bos indicus) recipients.

Morphological Aspects and Storage of Dypsis leptocheilos (Hodel) Beentje & J. Dransf. (Arecaceae) Seeds

Dypsis leptocheilos (Hodel) Beentje & J. Dransf. palms are widely used in landscaping, however there is a lack of studies about its biology, especially on the morphology of its seedling disseminules and the ideal seed storage time without loss of viability. The objectives of this work were to describe the morphological aspects and to study the storage effect on the germination of D. leptocheilos seeds. The experiments were performed at FCAV/UNESP, Jaboticabal Campus, São Paulo State, Brazil. In order to obtain a morphology description 100 disseminules were sowed in vermiculite. The external and internal sides of the disseminules as well as the representative phases of the germination process were sketched with the help of a light chamber attached to a stereomicroscope. Five treatments were arranged in order to study the storage effects on the seeds (four months of storage and straight after harvest), with four replicates with 25 disseminules each (seeds with attached endocarp) in a completely randomized design. The germination test was conducted over a 140 days period and noted every two days. In order to calculate the germination percentage (% G) and the Germination Speed Index (GSI), the seeds were considered germinated when the germinative button appeared. The data were submitted to a polynomial regression analysis to verify the behavior of the variables over the storage period. The D. leptocheilos seeds have rounded shape, ruminate endosperm and hard consistency. The embryo is lateral, peripheral and relatively undifferentiated, with approximately 3 mm long and conical shape. The germination percentage increased from 17% for seeds sowed straight after harvest to 73% for those stored over a three-month period. For the GSI the increase was about 0.85%. It was concluded that the germination of D. leptocheilos is of an adjacent ligulate type. Furthermore, the seeds stored for 3 months at 14 degrees C showed both higher percentage and germination speed.

Seed anatomy and germination of Phoenix roebelenii O'Brien (Arecaceae)

O objetivo desse trabalho foi estudar a morfologia, anatomia e o processo germinativo de sementes de Phoenix roebelenii. Para o levantamento dos dados biométricos foram utilizadas 100 sementes de frutos recém-colhidos, deixados secar ao ar por um dia. Para a germinação, quatro repetições de 50 sementes tratadas com Vitavax-Thiran foram semeadas em bandejas de plástico, contendo Sphagnum sp. como substrato e mantidas sob condições ambientais de laboratório. Detalhes da morfologia da semente foram documentados com o uso de microscopia eletrônica de varredura e esquematizados com auxílio de câmara clara, acoplada ao estereomicroscópio. Foram confeccionadas lâminas permanentes com cortes do embrião, para o estudo de sua anatomia. As dimensões médias das sementes foram: 10,32mm comprimento, 5,21mm largura e 3,91mm espessura. O peso de 1000 sementes foi de 151,1g e 1kg continha 6600 unidades. O início da germinação variou entre 27 e 58 dias. As sementes são albuminosas, com endosperma duro e o embrião é pouco diferenciado, lateral e periférico. A germinação inicia-se pela abertura de um opérculo, através do qual é emitido o pecíolo cotiledonar com o eixo embrionário na extremidade. O pecíolo funciona, internamente, como um haustório, digerindo gradativamente o endosperma. Na sua parte posterior, desenvolve-se a plúmula, que emerge através de uma fenda. Nota-se o aparecimento de raízes secundárias na porção anterior da raiz primária.