Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane

To contribute to our understanding of the genome complexity of sugarcane, we undertook a large-scale expressed sequence tag (EST),program. More than 260,000 cDNA clones were partially sequenced from 26 standard cDNA libraries generated from different sugarcane tissues. After the processing of the sequences, 237,954 high-quality ESTs were identified. These ESTs were assembled into 43,141 putative transcripts. of the assembled sequences, 35.6% presented no matches with existing sequences in public databases. A global analysis of the whole SUCEST data set indicated that 14,409 assembled sequences (33% of the total) contained at least one cDNA clone with a full-length insert. Annotation of the 43,141 assembled sequences associated almost 50% of the putative identified sugarcane genes with protein metabolism, cellular communication/signal transduction, bioenergetics, and stress responses. Inspection of the translated assembled sequences for conserved protein domains revealed 40,821 amino acid sequences with 1415 Pfam domains. Reassembling the consensus sequences of the 43,141 transcripts revealed a 22% redundancy in the first assembling. This indicated that possibly 33,620 unique genes had been identified and indicated that >90% of the sugarcane expressed genes were tagged.

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

Decreased oxidative stress in patients with ulcerative colitis supplemented with fish oil omega-3 fatty acids

OBJECTIVE: the potential pathogenicity of free radicals may have a pivotal role in ulcerative colitis. Fish oil omega-3 fatty acids exert anti-inflammatory effects on patients with ulcerative colitis (UC), but the precise mechanism of the action of fish oil on oxidative stress is still controversial. The aim of the present work was to verify the blood oxidative stress in patients with UC and determine whether the association of sulfasalazine to fish oil omega-3 fatty acids is more effective than isolated use of sulfasalazine to reduce the oxidative stress.METHODS:, Nine patients (seven female and two male; me. an age = 40 +/- 11 y) with mild or moderate active UC were studied in a randomized crossover design. In addition to their usual medication (2 g/d of sulfasalazine), they received fish oil omega-3 fatty acids (4.5 g/d) or placebo for 2-mo treatment periods that were separated by 2 mo, when they only received sulfasalazine. Nine healthy individuals served as control subjects to study the oxidative stress status. Disease activity was assessed by laboratory indicators (C-reactive protein, alpha(1)-acid glycoprotein, alpha(1)-antitrypsin, erythrocyte sedimentation rate, albumin, hemoglobin, and platelet count), sigmoidoscopy, and histology scores. Analysis of oxidative stress was assessed by plasma chemiluminescence and erythrocyte lipid peroxidation, both induced by tert butyl hydroperoxide (t-BuOOH) and by plasma malondialdehyde. Antioxidant status was assayed by total plasma antioxidant capacity (TRAP) and microsomal lipid peroxidation inhibition (LPI). Superoxide dismutase (SOD) and catalase erythrocyte enzymatic activities were also determined.RESULTS: No significant changes were observed in any laboratory indicator or in the sigmoidoscopy or histology scores, with the exception of erythrocyte sedimentation rate, which decreased with both treatments. Oxidative stress was demonstrated by significant decreases in TRAP and LPI levels, increased chemiluminescence induced by t-BuOOH, and higher SOD activity in patients with UC. Treatment with fish oil omega-3 fatty acids reverted the chemiluminescence induced by t-BuOOH and LPI to baseline levels but that did not occur when patients received only sulfasalazine. Levels of plasma malondialdehyde, erythrocyte lipid peroxidation, and catalase were not different from those in the control group.CONCLUSIONS: the results indicated that plasma oxidative stress occurs in patients with UC, and there was a significant decrease when the patients used sulfasalazine plus fish oil omega-3 fatty acids. However, there was no improvement in most laboratory indicators, sigmoidoscopy, and histology scores. The results suggested that omega-3 fatty acids may act as free radical scavengers protecting the patients against the overall effect of oxidative stress. (C)Elsevier B.V. 2003.

Influence of Implant Angulation With Different Crowns on Stress Distribution

The aim of this study was to perform a photoelastic analysis of stress distribution on straight and angulated implants with different crowns (screwed and cemented). Three models were made of photoelastic resin PL-2: model 1: external hexagon implant 3.75 x 10.00 mm at 0 degrees; model 2: external hexagon implant 3.75 x 10.00 mm at 17 degrees; model 3: external hexagon implant 3.75 x 10.00 mm at 30 degrees. Axial and oblique (45 degrees) load (100 N) was applied with a universal testing machine. The photoelastic fringes on the models were recorded with a digital camera and visualized in a graphic software for qualitative analysis. The axial loading generated the same pattern of stress distribution. The highest stresses were concentrated between medium and apical thirds. The oblique loading generated a similar pattern of stress distribution in the models with similar implant angulation; the highest stress was located on the cervical region opposite to implant angulation and on the apical third. It was concluded that the higher the implant angulation, the higher the stress value, independent of crown type. The screwed prostheses exhibited the highest stress concentration. The oblique load generated higher stress value and concentration than the axial load.

Photoelastic Analysis of Cemented or Screwed Implant-Supported Prostheses With Different Prostheses Connections

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

Effect of Passive Fit Absence in the Prosthesis/Implant/Retaining Screw System: A Two-Dimensional Finite Element Analysis

The misfit between prostheses and implants is a clinical reality, but the level that can be accepted without causing mechanical or biologic problem is not well defined. This study investigates the effect of different levels of unilateral angular misfit prostheses in the prosthesis/implant/retaining screw system and in the surrounding bone using finite element analysis. Four models of a two-dimensional finite element were constructed: group I (control), prosthesis that fit the implant; groups 2 to 4, prostheses with unilateral angular misfit of 50, 100, and 200 mu m, respectively. A load of 133 N was applied with a 30-degree angulation and off-axis at 2 mm from the long axis of the implant at the opposite direction of misfit on the models. Taking into account the increase of the angular misfit, the stress maps showed a gradual increase of prosthesis stress and uniform stress in the implant and trabecular bone. Concerning the displacement, an inclination of the system due to loading and misfit was observed. The decrease of the unilateral contact between prosthesis and implant leads to the displacement of the entire system, and distribution and magnitude alterations of the stress also occurred.

Comparison between complete denture and implant-retained overdenture: effect of different mucosa thickness and resiliency on stress distribution

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

Effect of different mucosa thickness and resiliency on stress distribution of implant-retained overdentures-2D FEA

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

Comparison of stress distribution between complete denture and implant-retained overdenture-2D FEA

The aim of this study was to compare the stress distribution induced by posterior functional loads on conventional complete dentures and implant-retained overdentures with different attachment systems using a two-dimentional Finite Element Analysis (FEA-2D). Three models representative of edentulous mandible were constructed on AutoCAD software; Group A (control), a model of edentulous mandible supporting a complete denture; Group B, a model of edentulous mandible supporting an overdenture over two splinted implants connected with the bar-clip system; Group C, a model of edentuluos mandible supporting an overdenture over two unsplinted impants with the O-ring system. Evaluation was conducted on Ansys software, with a vertical force of 100 N applied on the mandibular left first molar. When the stress was evaluated in supporting tissues, groups B (51.0 MPa) and C (52.6 MPa) demonstrated higher stress values than group A (10.1 MPa). Within the limits of this study, it may be conclued that the use of an attachment system increased stress values; furthermore, the use of splinted implants associated with the bar-clip attachment system favoured a lower stress distribution over the supporting tissue than the unsplinted implants with an O-ring abutment to retain the manibular overdenture.

Etch and rinse versus self-etching adhesives systems: Tridimensional micromechanical analysis of dentin/adhesive interface

The purpose of this study was to evaluate stress distribution in the hybrid layer produced by two adhesive systems using three-dimensional finite element analysis (FEA). Four FEA models (M) were developed: Mc, a representation of a dentin specimen (41 x 41 x 82 mu m) restored with composite resin, exhibiting the adhesive layer, hybrid layer (HL), resin tags, peritubular dentin, and intertubular dentin to simulate the etch-and-rinse adhesive system; Mr, similar to Mc, with lateral branches of the adhesive; Ma, similar to Mc, however without resin tags and obliterated tubule orifice, to simulate the environment for the self-etching adhesive system; Mat, similar to Ma, with tags. A numerical simulation was performed to obtain the maximum principal stress (sigma(max)). The highest sigma(max) in the HL was observed for the etch-and-rinse adhesive system. The lateral branches increased the sigma(max) in the HL. The resin tags had a little influence on stress distribution with the self-etching system. (C) 2012 Elsevier Ltd. All rights reserved.

Platform Switching: Biomechanical Evaluation Using Three-Dimensional Finite Element Analysis

Purpose: The objective of this study was to evaluate, using three-dimensional finite element analysis (3D FEA), the stress distribution in peri-implant bone tissue, implants, and prosthetic components of implant-supported single crowns with the use of the platform-switching concept. Materials and Methods: Three 3D finite element models were created to replicate an external-hexagonal implant system with peri-implant bone tissue in which three different implant-abutment configurations were represented. In the regular platform (RP) group, a regular 4.1-mm-diameter abutment (UCLA) was connected to regular 4.1-mm-diameter implant. The platform-switching (PS) group was simulated by the connection of a wide implant (5.0 mm diameter) to a regular 4.1-mm-diameter UCLA abutment. In the wide-platform (WP) group, a 5.0-mm-diameter UCLA abutment was connected to a 5.0-mm-diameter implant. An occlusal load of 100 N was applied either axially or obliquely on the models using ANSYS software. Results: Both the increase in implant diameter and the use of platform switching played roles in stress reduction. The PS group presented lower stress values than the RP and WP groups for bone and implant. In the peri-implant area, cortical bone exhibited a higher stress concentration than the trabecular bone in all models and both loading situations. Under oblique loading, higher intensity and greater distribution of stress were observed than under axial loading. Platform switching reduced von Mises (17.5% and 9.3% for axial and oblique loads, respectively), minimum (compressive) (19.4% for axial load and 21.9% for oblique load), and maximum (tensile) principal stress values (46.6% for axial load and 26.7% for oblique load) in the peri-implant bone tissue. Conclusion: Platform switching led to improved biomechanical stress distribution in peri-implant bone tissue. Oblique loads resulted in higher stress concentrations than axial loads for all models. Wide-diameter implants had a large influence in reducing stress values in the implant system. INT J ORAL MAXILLOFAC IMPLANTS 2011;26:482-491

Finite Element Analysis to Compare Complete Denture and Implant-Retained Overdentures With Different Attachment Systems

This finite element analysis compared stress distribution on complete dentures and implant-retained overdentures with different attachment systems. Four models of edentulous mandible were constructed: group A (control), complete denture; group B, overdenture retained by 2 splinted implants with bar-clip system; group C, overdenture retained by 2 unsplinted implants with o'ring system; and group D, overdenture retained by 2 splinted implants with bar-clip and 2 distally placed o'ring system. Evaluation was performed on Ansys software, with 100-N vertical load applied on central incisive teeth. The lowest maximum general stress value (in megapascal) was observed in group A (64.305) followed by groups C (119.006), D (258.650), and B (349.873). The same trend occurred it) supporting tissues with the highest stress value for cortical bone. Unsplinted implants associated with the o'ring attachment system showed the lowest maximum stress values among all overdenture groups. Furthermore, o'ring system also improved stress distribution when associated with bar-clip system.

Influence of Crown Ferrule Heights and Dowel Material Selection on the Mechanical Behavior of Root-Filled Teeth: A Finite Element Analysis

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

Evaluation of Stress Patterns Produced by Implant-Retained Overdentures and Implant-Retained Fixed Partial Denture

The purposes of this study were to photoelastically measure the biomechanical behavior of 4 implants retaining different cantilevered bar mandibular overdenture designs and to compare a fixed partial denture (FPD). A photoelastic model of a human edentulous mandible was fabricated, which contained 4 screw-type implants (3.75 x 10 mm) embedded in the parasymphyseal area. An FPD and 3 overdenture designs with the following attachments were evaluated: 3 plastic Hader clips, 1 Hader clip with 2 posterior resilient cap attachments, and 3 ball/O-ring attachments. Vertical occlusal forces of 100 N were applied between the central incisor and unilaterally to the right and left second premolars and second molars. Stresses that developed in the supporting structure were monitored photoelastically and recorded photographically. The results showed that the anterior loading, the overdenture with 3 plastic Hader clips, displayed the largest stress concentration at the medium implant. With premolar loading, the FPD and overdenture with 3 plastic Hader clips displayed the highest stresses to the ipsilateral terminal implant. With molar loading, the overdenture with 3 ball/O-ring attachments displayed the most uniform stress distribution in the posterior edentulous ridge, with less overloading in the terminal implant. It was concluded that vertical forces applied to the bar-clip overdenture and FPD created immediate stress patterns of greater magnitude and concentration on the ipsilateral implants, whereas the ball/O-ring attachments transferred minimal stress to the implants. The increased cantilever in the FPD caused the highest stresses to the terminal implant.

Mechanical behavior of ceramic veneer in zirconia-based restorations: a 3-dimensional finite element analysis using microcomputed tomography data

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