Plant or fungal sequences? An alternative optimized PCR protocol to avoid ITS (nrDNA) misamplification

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

Atributos bioquímicos e químicos do solo rizosférico e não rizosférico de culturas em rotação no sistema de semeadura direta

Sistemas autossustentáveis favorecem as populações microbianas devido à conservação e ao aumento da matéria orgânica no solo. Além disso, as plantas que fazem parte desses sistemas promovem o efeito rizosférico, por meio da zona de influência das raízes, que resulta no aumento da atividade e na modificação da população microbiana. O objetivo deste trabalho foi avaliar o efeito da rotação de culturas de inverno sobre sequências de verão, em sistema de semeadura direta, nos atributos bioquímicos (amilase, urease, celulase e protease) e químicos (carbono orgânico total - COT, carboidratos totais e proteínas totais) em solo rizosférico (SR) e não rizosférico (SNR). Este estudo foi constituído de três culturas de inverno: milho (Zea mays L.), girassol (Helianthus anuus L.) e guandu (Cajanus cajan (L.) Millsp), que estavam em rotação sobre três sequências de verão: soja/soja (Glycine max L.), milho/milho e soja/milho, e duas posições no solo: solo aderido às raízes das plantas (SR) e solo da entrelinha de plantio (SNR). As atividades da amilase, celulase, protease e urease no SR foram 16, 85, 62 e 100 % maiores do que no SNR; para COT e proteínas totais a diferença foi de 21 %. Das culturas de inverno, o milho foi a que mais estimulou as atividades das enzimas amilase, celulase, urease e protease no SR, bem como a atividade das enzimas amilase, urease e protease no SNR. de modo geral, os teores de proteínas totais não foram influenciados pelas culturas de inverno e pelas sequências de verão; os carboidratos totais foram influenciados pelas culturas de inverno milho e girassol. Para o COT houve influência apenas da sequência de verão milho/milho. Os atributos bioquímicos e químicos avaliados neste estudo podem ser utilizados como indicadores das alterações no solo promovidas pelas culturas de inverno e pelas sequências de verão.

Crop sequences in no-tillage system: effects on soil fertility and soybean, maize and rice yield

Os resíduos vegetais das culturas, ao se decomporem, alteram os atributos químicos do solo e, como consequência, influenciam a produtividade das culturas em sucessão. O objetivo deste trabalho foi avaliar os atributos químicos do solo e a produtividade das culturas de soja, milho e arroz, cultivadas no verão, em sucessão a culturas de inverno em semeadura direta. O experimento foi realizado em Jaboticabal-SP (48 ° 18 ' 58 '' W e 21 ° 15 ' 22 '' S), em um Latossolo Vermelho eutrófico. O delineamento experimental foi em blocos ao acaso, no esquema em faixas, com três repetições. Os tratamentos foram constituídos pela combinação de quatro sequências de culturas de verão (monoculturas de milho e soja e rotações soja/milho e arroz/feijão/algodão) com sete culturas de inverno (milho, girassol, nabo forrageiro, milheto, guandu, sorgo e crotalária). Os cultivos iniciaram-se em 2002. Após o manejo das culturas de inverno e antes da semeadura das culturas de verão do ano agrícola 2006/2007, foram coletadas amostras de solo nas camadas de 0-2,5; 2,5-5,0; 5-10; 10-20; e 20-30 cm. Nas amostras de solo, foram determinados: teores de matéria orgânica, pH, teores de P (resina), K, Ca e Mg trocáveis e acidez potencial (H + Al). As sequências de verão rotação soja/milho e milho em monocultura proporcionaram no solo menores teores de matéria orgânica na camada de 0-10 cm e de P do solo na camada de 0-20 cm. Na sequência de verão arroz/feijão/algodão, maiores teores de K foram proporcionados pelas culturas de inverno crotalária e nabo forrageiro, na camada de 0-10 cm, e milheto, na de 0-2,5 cm. Crotalária, milheto, nabo forrageiro e sorgo, cultivados no inverno, proporcionaram maiores teores de matéria orgânica no solo na camada de 0-30 cm. Maiores teores de P no solo foram proporcionados pela crotalária, na camada de 0-2,5 cm, e pelo nabo forrageiro, na de 0-5 cm. Maiores produtividades de soja, como monocultura de verão, foram obtidas após nabo forrageiro e crotalária e, quando em rotação com milho no verão, após nabo forrageiro, crotalária e milheto. Maiores produtividades de milho foram obtidas após nabo forrageiro, milheto e guandu, e menor produtividade de arroz foi obtida após sorgo.

Odometria visual baseada em técnicas de structure from motion

Visual Odometry is the process that estimates camera position and orientation based solely on images and in features (projections of visual landmarks present in the scene) extraced from them. With the increasing advance of Computer Vision algorithms and computer processing power, the subarea known as Structure from Motion (SFM) started to supply mathematical tools composing localization systems for robotics and Augmented Reality applications, in contrast with its initial purpose of being used in inherently offline solutions aiming 3D reconstruction and image based modelling. In that way, this work proposes a pipeline to obtain relative position featuring a previously calibrated camera as positional sensor and based entirely on models and algorithms from SFM. Techniques usually applied in camera localization systems such as Kalman filters and particle filters are not used, making unnecessary additional information like probabilistic models for camera state transition. Experiments assessing both 3D reconstruction quality and camera position estimated by the system were performed, in which image sequences captured in reallistic scenarios were processed and compared to localization data gathered from a mobile robotic platform

Increasing trends of sleep complaints in the city of São Paulo, Brazil

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

Efeitos da interação dipolar na nucleação de vórtices em nano-cilindros magnéticos

The effect of confinement on the magnetic structure of vortices of dipolar coupled ferromagnetic nanoelements is an issue of current interest, not only for academic reasons, but also for the potential impact in a number of promising applications. Most applications, such as nano-oscillators for wireless data transmission, benefit from the possibility of tailoring the vortex core magnetic pattern. We report a theoretical study of vortex nucleation in pairs of coaxial iron and Permalloy cylinders, with diameters ranging from 21nm to 150nm, and 12nm and 21nm thicknesses, separated by a non-magnetic layer. 12nm thick iron and Permalloy isolated (single) cylinders do not hold a vortex, and 21nm isolated cylinders hold a vortex. Our results indicate that one may tailor the magnetic structure of the vortices, and the relative chirality, by selecting the thickness of the non-magnetic spacer and the values of the cylinders diameters and thicknesses. Also, the dipolar interaction may induce vortex formation in pairs of 12nm thick nanocylinders and inhibit the formation of vortices in pairs of 21nm thick nanocylinders. These new phases are formed according to the value of the distance between the cylinderes. Furthermore, we show that the preparation route may control relative chirality and polarity of the vortex pair. For instance: by saturating a pair of Fe 81nm diameter, 21nm thickness cylinders, along the crystalline anisotropy direction, a pair of 36nm core diameter vortices, with same chirality and polarity is prepared. By saturating along the perpendicular direction, one prepares a 30nm diameter core vortex pair, with opposite chirality and opposite polarity. We also present a theoretical discussion of the impact of vortices on the thermal hysteresis of a pair of interface biased elliptical iron nanoelements, separated by an ultrathin nonmagnetic insulating layer. We have found that iron nanoelements exchange coupled to a noncompensated NiO substrate, display thermal hysteresis at room temperature, well below the iron Curie temperature. The thermal hysteresis consists in different sequences of magnetic states in the heating and cooling branches of a thermal loop, and originates in the thermal reduction of the interface field, and on the rearrangements of the magnetic structure at high temperatures, 5 produce by the strong dipolar coupling. The width of the thermal hysteresis varies from 500 K to 100 K for lateral dimensions of 125 nm x 65 nm and 145 nm x 65 nm. We focus on the thermal effects on two particular states: the antiparallel state, which has, at low temperatures, the interface biased nanoelement with the magnetization aligned with the interface field and the second nanoelement aligned opposite to the interface field; and in the parallel state, which has both nanoelements with the magnetization aligned with the interface field at low temperatures. We show that the dipolar interaction leads to enhanced thermal stability of the antiparallel state, and reduces the thermal stability of the parallel state. These states are the key phases in the application of pairs of ferromagnetic nanoelements, separated by a thin insulating layer, for tunneling magnetic memory cells. We have found that for a pair of 125nm x 65nm nanoelements, separated by 1.1nm, and low temperature interface field strength of 5.88kOe, the low temperature state (T = 100K) consists of a pair of nearly parallel buckle-states. This low temperature phase is kept with minor changes up to T= 249 K when the magnetization is reduced to 50% of the low temperature value due to nucleation of a vortex centered around the middle of the free surface nanoelement. By further increasing the temperature, there is another small change in the magnetization due to vortex motion. Apart from minor changes in the vortex position, the high temperature vortex state remains stable, in the cooling branch, down to low temperatures. We note that wide loop thermal hysteresis may pose limits on the design of tunneling magnetic memory cells

Increasing Moodle Resources Through Cloud Computing

The increase of higher education offer is a basic need of developed and emerging countries. It requires increasing and ongoing investments. The offer of higher education, by means of Distance Learning, based on the Internet, is one of the most efficient manners for the massification of this offer, as it allows ample coverage and lower costs. In this scenario, we highlight Moodle, an open and low-cost environment for Distance Learning. Its utilization may be amplified through the adoption of an emerging Information and Communication Technology (ICT), Cloud Computing, which allows the virtualization of Moodle sites, cutting costs, facilitating management and increasing its service capacity. This article diffuses a public tool, opened and free, for automatic conversion of Moodle sites, such that these may be hosted on Azure: the Cloud Computing environment of Microsoft.

Caracterização tectono-estratigráfica da sequência transicional na sub-bacia de Sergipe

This thesis deals with the tectonic-stratigraphic evolution of the Transitional Sequence in the Sergipe Sub-basin (the southern segment of the Sergipe-Alagoas Basin, Northeast Brazil), deposited in the time interval of the upper Alagoas/Aptian stage. Sequence boundaries and higher order internal sequences were identified, as well as the structures that affect or control its deposition. This integrated approach aimed to characterize the geodynamic setting and processes active during deposition of the Transitional Sequence, and its relations with the evolutionary tectonic stages recognized in the East Brazilian Margin basins. This subject addresses more general questions discussed in the literature, regarding the evolution from the Rift to the Drift stages, the expression and significance of the breakup unconformity, the relationships between sedimentation and tectonics at extensional settings, as well as the control on subsidence processes during this time interval. The tectonic-stratigraphic analysis of the Transitional Sequence was based on seismic sections and well logs, distributed along the Sergipe Sub-basin (SBSE). Geoseismic sections and seismic facies analysis, stratigraphic profiles and sections, were compiled through the main structural blocks of this sub-basin. These products support the depositional and tectonic-stratigraphic evolutionary models built for this sequence. The structural analysis highlighted similarities in deformation styles and kinematics during deposition of the Rift and Transitional sequences, pointing to continuing lithospheric extensional processes along a NW trend (X strain axis) until the end of deposition of the latter sequence was finished by the end of late Aptian. The late stage of extension/rifting was marked by (i) continuous (or as pulses) fault activity along the basin, controling subsidence and creation of depositional space, thereby characterizing upper crustal thinning and (ii) sagstyle deposition of the Transitional Sequence at a larger scale, reflecting the ductile stretching and thinnning of lower and sub crustal layers combined with an increasing importance of the thermal subsidence regime. Besides the late increments of rift tectonics, the Transitional Sequence is also affected by reactivation of the border faults of SBSE, during and after deposition of the Riachuelo Formation (lower section of the Transgressive Marine Sequence, of Albian age). It is possible that this reactivation reflects (through stress propagation along the newlycreated continental margin) the rifting processes still active further north, between the Alagoas Sub-basin and the Pernambuco-Paraíba Basin. The evaporitic beds of the Transitional Sequence contributed to the development of post-rift structures related to halokinesis and the continental margin collapse, affecting strata of the overlying marine sequences during the Middle Albian to the Maastrichtian, or even the Paleogene time interval. The stratigraphic analysis evidenced 5 depositional sequences of higher order, whose vertical succession indicates an upward increase of the base level, marked by deposition of continental siliciclastic systems overlain by lagunar-evaporitic and restricted marine systems, indicating that the Transitional Sequence was deposited during relative increase of the eustatic sea level. At a 2nd order cycle, the Transitional Sequence may represent the initial deposition of a Transgressive Systems Tract, whose passage to a Marine Transgressive Sequence would also be marked by the drowning of the depositional systems. At a 3rd order cycle, the sequence boundary corresponds to a local unconformity that laterally grades to a widespread correlative conformity. This boundary surface corresponds to a breakup unconformity , being equivalent to the Pre-Albian Unconformity at the SBSE and contrasting with the outstanding Pre-upper Alagoas Unconformity at the base of the Transitional Sequence; the latter is alternatively referred, in the literature, as the breakup unconformity. This Thesis supports the Pre-Albian Unconformity as marker of a major change in the (Rift-Drift) depositional and tectonic setting at SBSE, with equivalent but also diachronous boundary surfaces in other basins of the Atlantic margin. The Pre-upper Alagoas Unconformity developed due to astenosphere uplift (heating under high lithospheric extension rates) and post-dates the last major fault pulse and subsequent extensive block erosion. Later on, the number and net slip of active faults significantly decrease. At deep to ultra deep water basin segments, seaward-dipping reflectors (SDRs) are unconformably overlain by the seismic horizons correlated to the Transitional Sequence. The SDRs volcanic rocks overly (at least in part) continental crust and are tentatively ascribed to melting by adiabatic decompression of the rising astenospheric mantle. Even though being a major feature of SBSE (and possibly of other basins), the Pre-upper Alagoas Unconformity do not correspond to the end of lithospheric extension processes and beginning of seafloor spreading, as shown by the crustal-scale extensional structures that post-date the Transitional Sequence. Based on this whole context, deposition of the Transitional Sequence is better placed at a late interval of the Rift Stage, with the advance of an epicontinental sea over a crustal segment still undergoing extension. Along this segment, sedimentation was controled by a combination of thermal and mechanical subsidence. In continuation, the creation of oceanic lithosphere led to a decline in the mechanical subsidence component, extension was transferred to the mesoceanic ridge and the newly-formed continental margin (and the corresponding Marine Sequence) began to be controlled exclusively by the thermal subsidence component. Classical concepts, multidisciplinary data and new architectural and evolutionary crustal models can be reconciled and better understood under these lines

Comparison of the sequences of the internal transcribed Spacer regions and PbGP43 genes of Paracoccidioides brasiliensis from patients and armadillos (Dasypus novemcinctus)

Paracoccidioides brasiliensis isolates from 10 nine-banded armadillos (Dasypus novemcinctus) were comparable with 19 clinical isolates by sequence analysis of the PbGP43 gene and ribosomal internal transcribed spacer 1 (ITS1) and ITS2 and by random amplified polymorphic DNA. In this original ITS study, eight isolates differed by one or three sites among five total substitution sites.

EBNA-1 gene sequences in Brazilian and American patients with Hodgkin's disease

We examined the types of Epstein-Barr virus-associated nuclear antigen-1 (EBNA-1) gene carboxy (C)-terminal mutations occurring in Hodgkin's disease (HD) and reactive tissues from two different geographic regions. Previously reported EBNA-1 C-terminal region amino acid sequence variants, based on the amino acid at codon 487, include Prototype (P)-ala, which is found in the B95.8-derived prototype virus, P-thr, Variant (V)-leu, V-val, and V-pro. Using polymerase chain reaction (PCR) to amplify portions of the EBNA-1 gene, followed by DNA sequencing, we found a single EBNA-1 gene sequence variant in each tissue, whether reactive or neoplastic and whether from Brazil or the United States. Variant EBNA-1 gene sequences were more common in both neoplastic and non-neoplastic tissues from different geographic areas than the so-called prototype sequence. In the 17 Brazilian HD cases, 4 cases had P-thr variants and 13 had V-leu variants. In the six reactive tissues from Brazil, one had a P-ala variant, two had P-thr variants, and three had V-leu variants. In the 12 American HD cases, 2 had P-ala variants, 6 had P-thr variants, and 4 had V-leu variants. The 11 American reactive tissues included 2 P ala variants, 5 P-thr variants, and 4 V-leu variants. In both countries, there were similar variant EBNA-1 sequences present in normal tissues and HD cases. Compared with the P ala and P-thr cases, the V-leu cases were more likely to have the 30-bp latent membrane protein 1 (LMP1) gene deletion (P = 0.0075). In addition, cases of HD with the V-leu were statistically associated with a substitution of asparagine for glutamine at codon 322 of the C-terminal portion of the LMP1 gene. Our results suggest that any variation in EBNA-1 gene sequence is caused by a polymorphism present in pre-existing viral strains in the underlying population, and not a mutation occurring during oncogenesis. (C) 1999 by the American Society of Hematology.

Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp aurantifolii

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

Role of flanking sequences and phosphorylation in the recognition of the simian-virus-40 large T-antigen nuclear localization sequences by importin-alpha

The nuclear import of simian-virus-40 large T-antigen (tumour antigen) is enhanced via phosphorylation by the protein kinase CK2 at Ser(112) in the vicinity of the NLS (nuclear localization sequence). To determine the structural basis of the effect of the sequences flanking the basic cluster KKKRK, and the effect of phosphorylation on the recognition of the NLS by the nuclear import factor importin-alpha (Impalpha), we co-crystallized non-autoinhibited Impalpha with peptides corresponding to the phosphorylated and non-phosphorylated forms of the NLS, and determined the crystal structures of the complexes. The structures show that the amino acids N-terminally flanking the basic cluster make specific contacts with the receptor that are distinct from the interactions between bipartite NLSs and Impalpha. We confirm the important role of flanking sequences using binding assays. Unexpectedly, the regions of the peptides containing the phosphorylation site do not make specific contacts with the receptor. Binding assays confirm that phosphorylation does not increase the affinity of the T-antigen NLS to Impalpha. We conclude that the sequences flanking the basic clusters in NLSs play a crucial role in nuclear import by modulating the recognition of the NLS by Impalpha, whereas phosphorylation of the T-antigen enhances nuclear import by a mechanism that does not involve a direct interaction of the phosphorylated residue with Impalpha.

Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTEs were assembled into 81,429 contigs. of these, 1,181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTEs sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTEs coincided with DNA regions predicted as encoding exons by GENSCAN.