Global analysis of the sugarcane microtranscriptome reveals a unique composition of small RNAs associated with axillary bud outgrowth

Axillary bud outgrowth determines shoot architecture and is under the control of endogenous hormones and a fine-tuned gene-expression network, which probably includes small RNAs (sRNAs). Although it is well known that sRNAs act broadly in plant development, our understanding about their roles in vegetative bud outgrowth remains limited. Moreover, the expression profiles of microRNAs (miRNAs) and their targets within axillary buds are largely unknown. Here, we employed sRNA next-generation sequencing as well as computational and gene-expression analysis to identify and quantify sRNAs and their targets in vegetative axillary buds of the biofuel crop sugarcane (Saccharum spp.). Computational analysis allowed the identification of 26 conserved miRNA families and two putative novel miRNAs, as well as a number of trans-acting small interfering RNAs. sRNAs associated with transposable elements and protein-encoding genes were similarly represented in both inactive and developing bud libraries. Conversely, sequencing and quantitative reverse transcription-PCR results revealed that specific miRNAs were differentially expressed in developing buds, and some correlated negatively with the expression of their targets at specific stages of axillary bud development. For instance, the expression patterns of miR159 and its target GAMYB suggested that they may play roles in regulating abscisic acid-signalling pathways during sugarcane bud outgrowth. Our work reveals, for the first time, differences in the composition and expression profiles of diverse sRNAs and targets between inactive and developing vegetative buds that, together with the endogenous balance of specific hormones, may be important in regulating axillary bud outgrowth. © 2013 © The Author(2) [2013].

The Lord of the rings e a estética da finitude

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Da Camelot arturiana à Terra-média: representações da mulher em Le morte Darthur e the Lord of the rings

Pós-graduação em Letras - IBILCE

Análisis morfométrico, merístico, filogenético y filogeográfico del caballo de mar Hippocampus reidi (Ginsburg 1933) (Teleostei: Sygnathidae) de la costa nororiental da Venezuela

Pós-graduação em Ciências Biológicas (Zoologia) - IBB

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

Background: Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data.Results: Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. We assumed that the most abundant tandem repeat is the centromere DNA, which was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond approximately 50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution.Conclusions: While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animal and plant genomes. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes.

eIF5A and EF-P: two unique translation factors are now traveling the same road

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

Respiratory manifestations of panic disorder in animals and humans: A unique opportunity to understand how supramedullary structures regulate breathing

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

Digit systems over commutative rings

Let epsilon be a commutative ring with identity and P is an element of epsilon[x] be a polynomial. In the present paper we consider digit representations in the residue class ring epsilon[x]/(P). In particular, we are interested in the question whether each A is an element of epsilon[x]/(P) can be represented modulo P in the form e(0)+ e(1)x + ... + e(h)x(h), where the e(i) is an element of epsilon[x]/(P) are taken from a fixed finite set of digits. This general concept generalizes both canonical number systems and digit systems over finite fields. Due to the fact that we do not assume that 0 is an element of the digit set and that P need not be monic, several new phenomena occur in this context.

Construction and decoding of BCH codes over chain of commutative rings

In this paper, we present a new construction and decoding of BCH codes over certain rings. Thus, for a nonnegative integer t, let A0 ⊂ A1 ⊂···⊂ At−1 ⊂ At be a chain of unitary commutative rings, where each Ai is constructed by the direct product of appropriate Galois rings, and its projection to the fields is K0 ⊂ K1 ⊂···⊂ Kt−1 ⊂ Kt (another chain of unitary commutative rings), where each Ki is made by the direct product of corresponding residue fields of given Galois rings. Also, A∗ i and K∗ i are the groups of units of Ai and Ki, respectively. This correspondence presents a construction technique of generator polynomials of the sequence of Bose, Chaudhuri, and Hocquenghem (BCH) codes possessing entries from A∗ i and K∗ i for each i, where 0 ≤ i ≤ t. By the construction of BCH codes, we are confined to get the best code rate and error correction capability; however, the proposed contribution offers a choice to opt a worthy BCH code concerning code rate and error correction capability. In the second phase, we extend the modified Berlekamp-Massey algorithm for the above chains of unitary commutative local rings in such a way that the error will be corrected of the sequences of codewords from the sequences of BCH codes at once. This process is not much different than the original one, but it deals a sequence of codewords from the sequence of codes over the chain of Galois rings.

A note on units of finite local rings in an ascending chain

In this paper we present matrices over unitary finite commutative local rings connected through an ascending chain of containments, whose elements are units of the corresponding rings in the chain such that the McCoy ranks are the largest ones.

Linear codes over finite local rings in a chain

For a positive integer $t$, let \begin{equation*} \begin{array}{ccccccccc} (\mathcal{A}_{0},\mathcal{M}_{0}) & \subseteq & (\mathcal{A}_{1},\mathcal{M}_{1}) & \subseteq & & \subseteq & (\mathcal{A}_{t-1},\mathcal{M}_{t-1}) & \subseteq & (\mathcal{A},\mathcal{M}) \\ \cap & & \cap & & & & \cap & & \cap \\ (\mathcal{R}_{0},\mathcal{M}_{0}^{2}) & & (\mathcal{R}_{1},\mathcal{M}_{1}^{2}) & & & & (\mathcal{R}_{t-1},\mathcal{M}_{t-1}^{2}) & & (\mathcal{R},\mathcal{M}^{2}) \end{array} \end{equation*} be a chain of unitary local commutative rings $(\mathcal{A}_{i},\mathcal{M}_{i})$ with their corresponding Galois ring extensions $(\mathcal{R}_{i},\mathcal{M}_{i}^{2})$, for $i=0,1,\cdots,t$. In this paper, we have given a construction technique of the cyclic, BCH, alternant, Goppa and Srivastava codes over these rings. Though, initially in \cite{AP} it is for local ring $(\mathcal{A},\mathcal{M})$, in this paper, this new approach have given a choice in selection of most suitable code in error corrections and code rate perspectives.

A Note on Linear Codes over Semigroup Rings

In this paper, we introduced new construction techniques of BCH, alternant, Goppa, Srivastava codes through the semigroup ring B[X; 1 3Z0] instead of the polynomial ring B[X; Z0], where B is a finite commutative ring with identity, and for these constructions we improve the several results of [1]. After this, we present a decoding principle for BCH, alternant and Goppa codes which is based on modified Berlekamp-Massey algorithm. This algorithm corrects all errors up to the Hamming weight t ≤ r/2, i.e., whose minimum Hamming distance is r + 1.

Quaternion orders over quadratic integer rings from arithmetic fuchsian groups

In this paper we show that the quaternion orders OZ[ √ 2] ≃ ( √ 2, −1)Z[ √ 2] and OZ[ √ 3] ≃ (3 + 2√ 3, −1)Z[ √ 3], appearing in problems related to the coding theory [4], [3], are not maximal orders in the quaternion algebras AQ( √ 2) ≃ ( √ 2, −1)Q( √ 2) and AQ( √ 3) ≃ (3 + 2√ 3, −1)Q( √ 3), respectively. Furthermore, we identify the maximal orders containing these orders.

Chauliocheilos saxatilis, a new genus and species of Hypoptopomatinae from rio Jequitinhonha basin, with a unique labial appendix (Teleostei: Loricariidae)

Chauliocheilos saxatilis, new genus and species, is described from headwater streams of the rio Itamarandiba, upper rio Jequitinhonha basin, southeastern Brazil. The new genus is diagnosed from all other Loricariidae members by having a unique labial appendix at laterodorsal portion of lower lip, associated to the proximal region of insertion of the maxillary barbel. From all Hypoptopomatinae genera, Chauliocheilos can be distinguished by having two additional series of lateral plates, one between the dorsal and mid-dorsal series, and the other between the mid-ventral and ventral series. In addition, the great number of lateral plates, the absence of the iris operculum, and the posterior dorsal-fin insertion contacting the neural spine of eighth vertebra, are other useful features to recognize the genus. The phylogenetic position of Chauliocheilos among the Hypoptopomatinae, as well as the morphology and possible functions of the labial appendix, are discussed.

Purification and characterization of a unique pectin lyase from aspergillus giganteus able to release unsaturated monogalacturonate during pectin degradation

A pectin lyase, named PLIII, was purified to homogeneity from the culture filtrate of Aspergillus giganteus grown in submerged culture containing orange peel waste as carbon source. PLIII was able to digest apple pectin and citrus pectins with different degrees of methyl esterification. Interestingly, the PLIII activity was stimulated in the presence of some divalent cations including Pb(2+) and was not significantly affected by Hg(2+). Like other pectin lyases, PLIII is stimulated by but is not dependent on Ca(2+). The main soluble product released during the degradation of pectic substances promoted by the PLIII is compatible with an unsaturated monogalacturonate. PLIII is a unique enzyme able to release unsaturated monogalacturonate as the only soluble product during the degradation of pectic substances; therefore, PLIII was classified as an exo-pectin lyase. To our knowledge, this is the first characterization of an exo-pectin lyase. The PLIII described in this work is potentially useful for ethanol production from pectin-rich biomass, besides other common applications for alkaline pectinases like preparation of textile fibers, coffee and tea fermentation, vegetable oil extraction, and the treatment of pulp in papermaking.