Plant U13 orthologues and orphan snoRNAs identified by RNomics of RNA from Arabidopsis nucleoli

Small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs (scaRNAs) are non-coding RNAs whose main function in eukaryotes is to guide the modification of nucleotides in ribosomal and spliceosomal small nuclear RNAs, respectively. Full-length sequences of Arabidopsis snoRNAs and scaRNAs have been obtained from cDNA libraries of capped and uncapped small RNAs using RNA from isolated nucleoli from Arabidopsis cell cultures. We have identified 31 novel snoRNA genes (9 box C/D and 22 box H/ACA) and 15 new variants of previously described snoRNAs. Three related capped snoRNAs with a distinct gene organization and structure were identified as orthologues of animal U13snoRNAs. In addition, eight of the novel genes had no complementarity to rRNAs or snRNAs and are therefore putative orphan snoRNAs potentially reflecting wider functions for these RNAs. The nucleolar localization of a number of the snoRNAs and the localization to nuclear bodies of two putative scaRNAs was confirmed by in situ hybridization. The majority of the novel snoRNA genes were found in new gene clusters or as part of previously described clusters. These results expand the repertoire of Arabidopsis snoRNAs to 188 snoRNA genes with 294 gene variants.

Carbon addition alters vegetation composition on ex-arable fields

1. Recent changes in European agricultural policy have led to measures to reverse the loss of species-rich grasslands through the creation of new areas on ex-arable land. Ex-arable soils are often characterized by high inorganic nitrogen (N) levels, which lead to the rapid establishment of annual and fast-growing perennial species during the initial phase of habitat creation. The addition of carbon (C) to the soil has been suggested as a countermeasure to reduce plant-available N and alter competitive interactions among plant species. 2. To test the effect of C addition on habitat creation on ex-arable land, an experiment was set up on two recently abandoned fields in Switzerland and on two 6-year-old restoration sites in the UK. Carbon was added as a mixture of either sugar and sawdust or wood chips and sawdust during a period of 2 years. The effects of C addition on soil parameters and vegetation composition were assessed during the period of C additions and 1 year thereafter. 3. Soil nitrate concentrations were reduced at all sites within weeks of the first C addition, and remained low until cessation of the C additions. The overall effect of C addition on vegetation was a reduction in above-ground biomass and cover. At the Swiss sites, the addition of sugar and sawdust led to a relative increase in legume and forb cover and to a decrease in grass cover. The soil N availability, composition of soil micro-organisms and vegetation characteristics continued to be affected after cessation of C additions. 4. Synthesis and applications. The results suggest that C addition in grassland restoration is a useful management method to reduce N availability on ex-arable land. Carbon addition alters the vegetation composition by creating gaps in the vegetation that facilitates the establishment of late-seral plant species, and is most effective when started immediately after the abandonment of arable fields and applied over several years.

The poliovirus 2C cis-acting replication element-mediated uridylylation of VPg is not required for synthesis of negative-sense genomes

Nucleotides in the terminal loop of the poliovirus 2C cis-acting replication element (2C(CRE)), a 61 nt structured RNA, function as the template for the addition of two uridylate (U) residues to the viral protein VPg. This uridylylation reaction leads to the formation of VPgpUpU, which is used by the viral RNA polymerase as a nucleotide-peptide primer for genome replication. Although VPg primes both positive- and negative-strand replication, the specific requirement for 2C(CRE)-mediated uridylylation for one or both events has not been demonstrated. We have used a cell-free in vitro translation and replication reaction to demonstrate that 2C(CRE) is not required for the initiation of the negative-sense strand, which is synthesized in the absence of 2C(CRE)-mediated VPgpUpU formation. We propose that the 3' poly(A) tail could serve as the template for the formation of a VPg-poly(U) primer that functions in the initiation of negative-sense strands.

Effects of hydrocolloid addition and high pressure processing on the rheological properties and microstructure of a commercial ostrich meat product "Yor" (Thai sausage)

"Yor" is a traditional sausage like product widely consumed in Thailand. Its textures are usually set by steaming, in this experiment ultra-high pressure was used to modify the product. Three types of hydrocolloid; carboxymethylcellulose (CMC), locust bean gum (LBG) and xanthan gum, were added to minced ostrich meat batter at concentration of 0-1% and subjected to high pressure 600 Mpa, 50 degrees C, 40 min. The treated samples were analysed for storage (G) and loss (G '') moduli by dynamic oscillatory testing as well as creep compliance for control stress measurement. Their microstructures using confocal microscopy were also examined. Hydrocolloid addition caused a significant (P < 0.05) decrease in both the G' and G '' moduli. However the loss tangent of all samples remained unchanged. Addition of hydrocolloids led to decreases in the gel network formation but appears to function as surfactant materials during the initial mixing stage as shown by the microstructure. Confocal microscopy suggested that the size of the fat droplets decreased with gum addition. The fat droplets were smallest on the addition of xanthan gum and increased in the order CMC, LBG and no added gum, respectively. Creep parameters of ostrich yors with four levels of xanthan gum addition (0.50%, 0.75%, 1.00% and 1.25%) showed an increase in the instantaneous compliance (J(0)), the retarded compliance (J(1)) and retardation time (lambda(1)) but a decrease in the viscosity (eta(0)) with increasing levels of addition. The results also suggested that the larger deformations used during creep testing might be more helpful in assessing the mechanical properties of the product than the small deformations used in oscillatory rheology. (c) 2007 Elsevier Ltd. All rights reserved.

Roles of the translationally controlled tumour protein (TCTP) and the double-stranded RNA-dependent protein kinase, PKR, in cellular stress responses

Translationally controlled tumour protein (TCTP) is a highly conserved protein present in all eukaryotic organisms. Various cellular functions and molecular interactions have been ascribed to this protein, many related to its growth-promoting and antiapoptotic properties. TCTP levels are highly regulated in response to various cellular stimuli and stresses. We have shown recently that the double-stranded RNA-dependent protein kinase, PKR, is involved in translational regulation of TCTP. Here we extend these studies by demonstrating that TCTP is downregulated in response to various proapoptotic treatments, in particular agents that induce Ca++ stress, in a PKR-dependent manner. This regulation requires phosphorylation of protein synthesis factor eIF2α. Since TCTP has been characterized as an antiapoptotic and Ca++-binding protein, we asked whether it is involved in protecting cells from Ca++-stress-induced apoptosis. Overexpression of TCTP partially protects cells against thapsigargin-induced apoptosis, as measured using caspase-3 activation assays, a nuclear fragmentation assay, using fluorescence-activated cell sorting analysis, and time-lapse video microscopy. TCTP also protects cells against the proapoptotic effects of tunicamycin and etoposide, but not against those of arsenite. Our results imply that cellular TCTP levels influence sensitivity to apoptosis and that PKR may exert its proapoptotic effects at least in part through downregulation of TCTP via eIF2α phosphorylation.

Cell walls of developing wheat starchy endosperm: comparison of composition and RNA-Seq transcriptome

The transcriptome of the developing starchy endosperm of hexaploid wheat (Triticum aestivum) was determined using RNA-Seq isolated at five stages during grain fill. This resource represents an excellent way to identify candidate genes responsible for the starchy endosperm cell wall, which is dominated by arabinoxylan (AX), accounting for 70% of the cell wall polysaccharides, with 20% (1,3; 1,4)-beta-D-glucan, 7% glucomannan, and 4% cellulose. A complete inventory of transcripts of 124 glycosyltransferase (GT) and 72 glycosylhydrolase (GH) genes associated with cell walls is presented. The most highly expressed GT transcript (excluding those known to be involved in starch synthesis) was a GT47 family transcript similar to Arabidopsis (Arabidopsis thaliana) IRX10 involved in xylan extension, and the second most abundant was a GT61. Profiles for GT43 IRX9 and IRX14 putative orthologs were consistent with roles in AX synthesis. Low abundances were found for transcripts from genes in the acyl-coA transferase BAHD family, for which a role in AX feruloylation has been postulated. The relative expression of these was much greater in whole grain compared with starchy endosperm, correlating with the levels of bound ferulate. Transcripts associated with callose (GSL), cellulose (CESA), pectin (GAUT), and glucomannan (CSLA) synthesis were also abundant in starchy endosperm, while the corresponding cell wall polysaccharides were confirmed as low abundance (glucomannan and callose) or undetectable (pectin) in these samples. Abundant transcripts from GH families associated with the hydrolysis of these polysaccharides were also present, suggesting that they may be rapidly turned over. Abundant transcripts in the GT31 family may be responsible for the addition of Gal residues to arabinogalactan peptide.

Detection of Leishmania (Leishmania) infantum RNA in fleas and ticks collected from naturally infected dogs

The occurrence of the insect vector (sand flies) with low rates of Leishmania infection, as well as autochthonous transmission in the absence of the natural vector in dogs, have been reported. These unexpected data suggest a hypothesis of other arthropods as a possible way of Leishmania transmission. The prevalence of Leishmania (Leishmania) infantum in fleas and ticks collected from dogs with canine visceral leishmaniasis (CVL), as well as parasite viability, were evaluated herein. The presence of L. (L.) infantum was assayed by PCR and ELISA in ectoparasites and biological samples from 73 dogs living in a Brazilian endemic area. As the occurrence of Leishmania DNA in ticks and fleas is expected given their blood-feeding habits, we next investigated whether parasites can remain viable inside ticks. PCR and ELISA confirmed that 83% of the dogs had CVL. Fleas and ticks (nymphs, male and female adults) were collected in 55% and 63% of the 73 dogs, respectively. Out of the 60 dogs with CVL, 80% harbored ectoparasites infected with L. (L.) infantum. The infection rates of the ectoparasites were 23% and 50% for fleas and ticks, respectively. The RNA analysis of the extract from ticks left in laboratory conditions during 7 to 10 days after removal from CVL dogs showed that parasites were alive. In addition, live parasites were also detected inside adult ticks recently molted in laboratory conditions. These findings indicate a higher infection rate of L. (L.) infantum in ticks and fleas, but they do not conclusively demonstrate whether these ticks can act as vectors of CVL, despite the fact that their rates were higher than those previously described in Lutzomyia longipalpis. The presence of viable L. (L.) infantum in ticks suggests the possible importance of dog ectoparasites in CVL dissemination.

Towards an assessment of character interdependence in avian RNA phylogenetics: A general secondary structure model for the avian mitochondrial 16S rRNA

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

An interaction between two RNA binding proteins, Nab2 and Pub1, links mRNA Processing/Export and mRNA stability

mRNA stability is modulated by elements in the mRNA transcript and their cognate RNA binding proteins. Poly(U) binding protein 1 (Pub1) is a cytoplasmic Saccharomyces cerevisiae mRNA binding protein that stabilizes transcripts containing AU-rich elements (AREs) or stabilizer elements (STEs). In a yeast two-hybrid screen, we identified nuclear poly(A) binding protein 2 (Nab2) as being a Pub1-interacting protein. Nab2 is an essential nucleocytoplasmic shuttling mRNA binding protein that regulates poly(A) tail length and mRNA export. The interaction between Pub1 and Nab2 was confirmed by copurification and in vitro binding assays. The interaction is mediated by the Nab2 zinc finger domain. Analysis of the functional link between these proteins reveals that Nab2, like Pub1, can modulate the stability of specific mRNA transcripts. The half-life of the RPS16B transcript, an ARE-like sequence-containing Pub1 target, is decreased in both nab2-1 and nab2-67 mutants. In contrast, GCN4, an STE-containing Pub1 target, is not affected. Similar results were obtained for other ARE- and STE-containing Pub1 target transcripts. Further analysis reveals that the ARE-like sequence is necessary for Nab2-mediated transcript stabilization. These results suggest that Nab2 functions together with Pub1 to modulate mRNA stability and strengthen a model where nuclear events are coupled to the control of mRNA turnover in the cytoplasm.

Cloning and molecular characterization of Trypanosoma cruzi U2, U4, U5, and U6 small nuclear RNAs

Small nuclear RNAs (snRNAs) are important factors in the functioning of eukaryotic cells that form several small complexes with proteins; these ribonucleoprotein particles (U snRNPs) have an essential role in the pre-mRNA processing, particularly in splicing, catalyzed by spliceosomes, large RNA-protein complexes composed of various snRNPs. Even though they are well defined in mammals, snRNPs are still not totally characterized in certain trypanosomatids as Trypanosoma cruzi. For this reason we subjected snRNAs (U2, U4, U5, and U6) from T. cruzi epimastigotes to molecular characterization by polymerase chain reaction (PCR) and reverse transcription-PCR. These amplified sequences were cloned, sequenced, and compared with those other of trypanosomatids. Among these snRNAs, U5 was less conserved and U6 the most conserved. Their respective secondary structures were predicted and compared with known T. brucei structures. In addition, the copy number of each snRNA in the T. cruzi genome was characterized by Southern blotting.

Dinâmica populacional do caranguejo-uçá, Ucides cordatus (Linnaeus, 1763) (CRUSTACEA, BRACHYURA, UCIDIDAE) no município de Porto do Mangue, litoral norte do estado do Rio Grande do Norte

Decapod crustaceans are one of the most important portions of megafaunal of coastal waters, playing a role as modifier of the environment and controlling populations of other organisms. Among the Decapoda, crab (brachyuran) constitutes the dominant macrofauna of mangroves. Among brachyuran is the mangrove crab (Ucides cordatus, Linnaeus, 1763), which represents the main component of the macrofauna of mangroves, particularly in Northern and Northeastern Brazil. In Brazil, its distribution is known from the state of Amapá to the north of Santa Catarina. This species is distinguished by its economic importance, being one of the main fishing resources in Brazil, generating a significant impact on their natural populations. This reduction would result in loss of value to the product, preventing its commercialization. Although it´s great ecological and economic importance, there are few articles about the biological aspects of U. cordatus, mainly in the state of Rio Grande do Norte. This work aimed to study the population dynamics of the mangrove crab, Ucides cordatus (Linnaeus, 1763), in Conchas estuary, Porto do Mangue, northern coast of Rio Grande do Norte. During the period November 2009 to October 2010 the crabs were collected monthly, obeying predetermined lunar periods (new moon or full moon) in a mangrove area in Porto do Mangue - RN. With the aid of a steel caliper (0.01 mm) and a precision balance (0.01 g) were measured biometric variables related to the animal's carapace, major propodus chela, width of abdomen (female), length of gonopodium ( males) and total weight. In addition, it was recorded, the gonads and molt stages, for males and females. In total, 476 crabs were collected, with 338 males and 138 females. Males were larger, heavier and in greater proportion than females. The reproductive period for the species in this location was limited during the months November to May, suggesting a change in current environmental legislation for the closure period. Synchrony was observed between the morphological and physiological maturity with females maturing earlier, possibly, a reproductive strategy adopted, compared to the low fishing pressure in the area. The molting period occurred in the dry season peaking in October. The analysis of growth, based on the parameters of von Bertalanffy was calculated using the nonlinear fit using modes (AJMOD). High growth rates for both males (L = 7.54 cm, k = 0.95, t0 =- 00:08; tmax = 4.84) and females (L = 6.50, k = 1 , 2, t0 =- 0008; tmax = 3.28) were found, contrasting with data from the literature, using other techniques. Males had higher asymptotic width size and longevity, but a lower growth constant when compared with females. The estimated age, for males and females, reaching the minimum capture size was 1.82 years and 1.63 years respectively. The size of physiological maturity, when individuals are able to reproduce, was estimated at 1.4 years and 1.05 years, for males and females, respectively. The recruitment period for this species is seasonal, with two peaks of occurrence, one in the rainy season and one in the dry season. This work represented the first effort on understanding the ecology of the mangrove crab, to the northern coast of Rio Grande do Norte. However, further studies on its biology should be undertaken, especially those related to growth, and recruitment, where observed that literature is more scarce

Cytoplasmic RNA and nuclear changes detected cytochemically during the degeneration of salivary glands of the tick Rhipicephalus sanguineus (Latreille, 1806) (Acari, Ixodidae)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

High-pressure granulites from Carire, Borborema Province, NE Brazil: Tectonic setting, metamorphic conditions and U-Pb, Lu-Hf and Sm-Nd geochronology

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

On the coupling of the self-dual field to dynamical U(1) matter and its dual theory

We consider arbitrary U (1) charged matter non-minimally coupled to the self-dual field in d = 2 + 1. The coupling includes a linear and a rather general quadratic term in the self-dual field. By using both Lagragian gauge embedding and master action approaches we derive the dual Maxwell Chern-Simons-type model and show the classical equivalence between the two theories. At the quantum level the master action approach in general requires the addition of an awkward extra term to the Maxwell Chern-Simons-type theory. Only in the case of a linear coupling in the self-dual field can the extra term be dropped and we are able to establish the quantum equivalence of gauge invariant correlation functions in both theories.