Copy number variation of individual cattle genomes using next-generation sequencing

Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising similar to 55.6-Mbp sequence-476 of which (similar to 38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (similar to 52%, chi(2) test; P-value <0.05). In contrast, genes related to pathogen- and parasite-resistance, such as CATHL4 and ULBP17, were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism, including APOL3 and FABP2, were highly duplicated in the beef breeds. These CNV regions also harbor genes like BPIFA2A (BSP30A) and WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health, and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome.

Reproductive cycle, ovarian development, and vertebrate-type steroids profile in the freshwater prawn Macrobrachium rosenbergii

This study is intended to characterize the ovarian development and hemolymph vertebrate-type steroids concentration during the reproductive cycle of the freshwater prawn, Macrobrachium rosenbergii. A five-stage classification based on the external observation of the ovary's size and color as seen through the tegument was used. The results showed the existence of a direct correspondence between the ovarian stages and the gonadosomatic index, the oöcyte diameter, and the characteristics of ovarian histology. In each stage total bleeding of the prawns was conducted and the hemolymph concentrations of 17β-estradiol (E 2), testosterone (T) and 17α-hydroxyprogesterone (17-OHP; conjugated and unconjugated) were determined by solid-phase radioimmunoassay (RIA). High levels of unconjugated 17-OHP, relatively constant concentrations of unconjugated T, and null concentration of unconjugated E 2 were found throughout the five stages considered. Nonetheless, low levels of E 2 were determined in all stages, in conjugated (glucoronide) form. The highest levels were obtained in stage II and III (18.14 ± 14.52 pg/ml hemolymph) and progressively declined in the other stages (7.53 ± 6.76 pg/ml hemolymph). These results point out the possible involvement of vertebrate-type steroids in the endocrine regulation of the Macrobrachium rosenbergii's ovarian cycle. To our knowledge this is the first study concerning the vertebrate-like steroid levels throughout the ovarian cycle and is a step needed to characterize the hemolymph profile of these steroids in order to elucidate the possible role in the regulation of the reproductive crustacean cycle.

Bait and habitat preferences, and temporal variability of social wasps (Hymenoptera: Vespidae) attracted to vertebrate carrion

In addition to feeding on carrion tissues and fluids, social wasps can also prey on immature and adult carrion flies, thereby reducing their populations and retarding the decomposition process of carcasses. In this study, we report on the occurrence and behavior of social wasps attracted to vertebrate carrion. The collections were made monthly from September 2006 to October 2007 in three environments (rural, urban, and forest) in six municipalities of southeast Brazil, using baited bottle traps. We collected Agelaia pallipes (Olivier, 1791) (n = 143), Agelaia vicina (Saussure, 1854) (n = 106), Agelaia multipicta (Haliday, 1836) (n = 18), and Polybia paulista Ihering, 1896 (n = 3). The wasps were observed feeding directly on the baits and preying on adult insects collected in the traps. Bait and habitat associations, temporal variability of social wasps, and possible forensic implications of their actions are discussed. © 2011 Entomological Society of America.

Description and interpretation of Cenozoic vertebrate ichnofossils in Rio Grande do Sul State, Brazil

In the neighborhood of the city of Boqueirão do Leão (State of Rio Grande do Sul, Brazil) a set of three big-sized tunnels has been found. One of the tunnels is only partially filled with sand and accessible along its entire length. It is horizontal, slightly sinuous, 36 m long, up to 4.2 m wide and up to 2.0 m high. The surface morphology of the walls is composed of anthropogenic marks, speleothems, black incrustations and traces like digging scratches and smoothed surfaces. The 2nd tunnel has its entrance blocked by sand and sandstone cobbles, but the end of the tunnel is only partially clogged and therefore accessible. This accessible portion is 12 m long, 3 m wide and 1.5 m high. The 3rd tunnel is completely filled and collapsed and is nowadays only indicated by concave roof features at its end. The general features of the tunnel system and the analysis of the surface morphology of the walls of the accessible portions permit to conclude that the tunnels were produced by ground sloths of the Cenozoic South American megafauna. The size of the tunnels suggests that its excavation was gradually carried out by successive generations of sloth herds, and not by a single individual animal. The primary function of the tunnels probably was not protection from predators, which had easy access to structures of this size, but to shelter during a drier climate. However, it is not yet possible to relate the tunnels to a specific ground sloth genus, a task that depends on the discovery of better-preserved tunnel systems. © 2013 by the Sociedade Brasileira de Paleontologia.

Evolutionary dynamics of retrotransposable elements Rex1, Rex3 and Rex6 in neotropical cichlid genomes

Background: Transposable elements (TEs) have the potential to produce broad changes in the genomes of their hosts, acting as a type of evolutionary toolbox and generating a collection of new regulatory and coding sequences. Several TE classes have been studied in Neotropical cichlids; however, the information gained from these studies is restricted to the physical chromosome mapping, whereas the genetic diversity of the TEs remains unknown. Therefore, the genomic organization of the non-LTR retrotransposons Rex1, Rex3, and Rex6 in five Amazonian cichlid species was evaluated using physical chromosome mapping and DNA sequencing to provide information about the role of TEs in the evolution of cichlid genomes. Results: Physical mapping revealed abundant TE clusters dispersed throughout the chromosomes. Furthermore, several species showed conspicuous clusters accumulation in the centromeric and terminal portions of the chromosomes. These TE chromosomal sites are associated with both heterochromatic and euchromatic regions. A higher number of Rex1 clusters were observed among the derived species. The Rex1 and Rex3 nucleotide sequences were more conserved in the basal species than in the derived species; however, this pattern was not observed in Rex6. In addition, it was possible to observe conserved blocks corresponding to the reverse transcriptase fragment of the Rex1 and Rex3 clones and to the endonuclease of Rex6. Conclusion: Our data showed no congruence between the Bayesian trees generated for Rex1, Rex3 and Rex6 of cichlid species and phylogenetic hypothesis described for the group. Rex1 and Rex3 nucleotide sequences were more conserved in the basal species whereas Rex6 exhibited high substitution rates in both basal and derived species. The distribution of Rex elements in cichlid genomes suggests that such elements are under the action of evolutionary mechanisms that lead to their accumulation in particular chromosome regions, mostly in heterochromatins. © 2013 Schneider et al.; licensee BioMed Central Ltd.

Identification of duplicated and stress-inducible Aox2b gene co-expressed with Aox1 in species of the Medicago genus reveals a regulation linked to gene rearrangement in leguminous genomes

In flowering plants, alternative oxidase (Aox) is encoded by 3-5 genes distributed in 2 subfamilies (Aox1 and Aox2). In several species only Aox1 is reported as a stress-responsive gene, but in the leguminous Vigna unguiculata Aox2b is also induced by stress. In this work we investigated the Aox genes from two leguminous species of the Medicago genus (Medicago sativa and Medicago truncatula) which present one Aox1, one Aox2a and an Aox2b duplication (named here Aox2b1 and Aox2b2). Expression analyses by semi-quantitative RT-PCR in M. sativa revealed that Aox1, Aox2b1 and Aox2b2 transcripts increased during seed germination. Similar analyses in leaves and roots under different treatments (SA, PEG, H2O2 and cysteine) revealed that these genes are also induced by stress, but with peculiar spatio-temporal differences. Aox1 and Aox2b1 showed basal levels of expression under control conditions and were induced by stress in leaves and roots. Aox2b2 presented a dual behavior, i.e., it was expressed only under stress conditions in leaves, and showed basal expression levels in roots that were induced by stress. Moreover, Aox2a was expressed at higher levels in leaves and during seed germination than in roots and appeared to be not responsive to stress. The Aox expression profiles obtained from a M. truncatula microarray dataset also revealed a stress-induced co-expression of Aox1, Aox2b1 and Aox2b2 in leaves and roots. These results reinforce the stress-inducible co-expression of Aox1/Aox2b in some leguminous plants. Comparative genomic analysis indicates that this regulation is linked to Aox1/Aox2b proximity in the genome as a result of the gene rearrangement that occurred in some leguminous plants during evolution. The differential expression of Aox2b1/2b2 suggests that a second gene has been originated by recent gene duplication with neofunctionalization. © 2013 Elsevier GmbH. All rights reserved.

Isolamento e caracterização de elementos transponíveis em espécies do gênero Brycon (Characidae, Bryconinae)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Evolução e organização genômica do gene FOXL2 em vertebrados

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

GABA and glutamate transporters: new events and function in the vertebrate retina

The neural retina is a highly complex tissue composed of excitatory and inhibitory neurons and glial cells. Glutamate, the main excitatory neurotransmitter, mediates information transfer from photoreceptors, bipolar cells, and ganglion cells, whereas interneurons, mainly amacrine and horizontal cells, use γ-aminobutyric acid (GABA), the main inhibitory neurotransmitter. In this review we place an emphasis on glutamate and GABA transporters as highly regulated molecules that play fundamental roles in neurotransmitter clearance, neurotransmitter release, and oxidative stress. We pharmacologically characterized glutamate transporters in chicken retina cells and identified two glutamate transporters: one Na+-dependent transporter and one Na+-independent transporter. The Na+-dependent uptake system presented characteristics related to the high-affinity xAG- system (EAAT1), and the Na+-independent uptake system presented characteristics related to the xCG- system, which highly contributes to glutamate transport in the retina. Glutamate shares the xCG- system with another amino acid, L-cysteine, suggesting the possible involvement of glutathione. Both transporter proteins are present mainly in Müller glial cells. GABA transporters (GATs) mediate high-affinity GABA uptake from the extracellular space and terminate the synaptic action of GABA in the central nervous system. GABA transporters can be modulated by molecules that act on specific sites to promote transporter phosphorylation and dephosphorylation. In addition to a role in the clearance of GABA, GATs may also release GABA through a reverse transport mechanism. In the chicken retina, a GAT-1 blocker, but not GAT2/3 blocker, was shown to inhibit GABA uptake, suggesting that GABA release from retina cells is mainly mediated by a GAT-1-like transporter.

Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes

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

Selective photoinactivation of Candida albicans in the non-vertebrate host infection model Galleria mellonella

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

The Quaternary vertebrate fauna of the limestone cave Gruta do Ioio, northeastern Brazil

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

ENDO-OLIGOPEPTIDASE-A, A PUTATIVE ENKEPHALIN-GENERATING ENZYME, IN THE VERTEBRATE RETINA

Endo-oligopeptidase A, EC 3.4.22.19, converts small enkephalin-containing peptides into the corresponding enkephalins in vitro. We investigated the presence of endooligopeptidase A in the retina and its possible colocalization with enkephalins in retinal neurons. The specific activity of endo-oligopeptidase A found in pigeon retinae (30.3 +/- 7.3 mU/mg, mean +/- standard deviation) was four times higher than in rabbit retinae (7.0 +/- 1.1 mU/mg). The enzyme activity was not modified by EDTA, but it was enhanced by dithiothreitol and inhibited by zinc and 5,5'-dithiobis(2-nitrobenzoic acid). Immunohistochemical experiments with a purified antiserum against rabbit endo-oligopeptidase A revealed labeled neurons in both the inner nuclear layer and the ganglion cell layer of pigeon and rabbit retinae. Double-labeling immunofluorescence experiments demonstrated that about 90% of neurons containing endo-oligopeptidase A-like immunoreactivity also contained [Leu5]-enkephalin-like immunoreactivity. These colocalization results may represent an important step toward the demonstration of the possible involvement of endo-oligopeptidase A in enkephalin generation in vivo.

Os papéis dos RNAs não codificantes no desenvolvimento embrionário: um panorama geral

The genome of multicellular organisms shows a ruge index of RNA transcripts that are not protein coding. These ncRNAs act in housekeeping and genic regulation, as well in signaling and cell differentiation, crucial events to embryonic and ontogenetic development. Moreover, another events require the orderly expression these transcripts, as in cromossomic inactivation and genomic imprinting process, and their fail may cause several syndromes, malformations, illness and even death of affected individual. This review focus is to present the main acting pathways of ncRNAs already studied, as well to introduce the actual landscape of Dapper gene cluster and its performance in vertebrate development.