In silico analysis of candidate genes involved in light sensing and signal transduction pathways in soybean

Several aspects of photoperception and light signal transduction have been elucidated by studies with model plants. However, the information available for economically important crops, such as Fabaceae species, is scarce. In order to incorporate the existing genomic tools into a strategy to advance soybean research, we have investigated publicly available expressed sequence tag ( EST) sequence databases in order to identify Glycine max sequences related to genes involved in light-regulated developmental control in model plants. Approximately 38,000 sequences from open-access databases were investigated, and all bona fide and putative photoreceptor gene families were found in soybean sequence databases. We have identified G. max orthologs for several families of transcriptional regulators and cytoplasmic proteins mediating photoreceptor-induced responses, although some important Arabidopsis phytochrome-signaling components are absent. Moreover, soybean and Arabidopsis gene-family homologs appear to have undergone a distinct expansion process in some cases. We propose a working model of light perception, signal transduction and response-eliciting in G. max, based on the identified key components from Arabidopsis. These results demonstrate the power of comparative genomics between model systems and crop species to elucidate several aspects of plant physiology and metabolism.

The BCD transient recorder revisited: firmware for the ISA-to-USB bridging card and software for the graphical user interface

This report describes recent updates to the custom-built data-acquisition hardware operated by the Center for Hypersonics. In 2006, an ISA-to-USB bridging card was developed as part of Luke Hillyard's final-year thesis. This card allows the hardware to be connected to any recent personal computers via a (USB or RS232) serial port and it provides a number of simple text-based commands for control of the hardware. A graphical user interface program was also updated to help the experimenter manage the data acquisition functions. Sampled data is stored in text files that have been compressed with the gzip for mat. To simplify the later archiving or transport of the data, all files specific to a shot are stored in a single directory. This includes a text file for the run description, the signal configuration file and the individual sampled-data files, one for each signal that was recorded.

Scalable Visualization of Galaxies, Oceans, and Brains

One of the challenges in scientific visualization is to generate software libraries suitable for the large-scale data emerging from tera-scale simulations and instruments. We describe the efforts currently under way at SDSC and NPACI to address these challenges. The scope of the SDSC project spans data handling, graphics, visualization, and scientific application domains. Components of the research focus on the following areas: intelligent data storage, layout and handling, using an associated “Floor-Plan” (meta data); performance optimization on parallel architectures; extension of SDSC’s scalable, parallel, direct volume renderer to allow perspective viewing; and interactive rendering of fractional images (“imagelets”), which facilitates the examination of large datasets. These concepts are coordinated within a data-visualization pipeline, which operates on component data blocks sized to fit within the available computing resources. A key feature of the scheme is that the meta data, which tag the data blocks, can be propagated and applied consistently. This is possible at the disk level, in distributing the computations across parallel processors; in “imagelet” composition; and in feature tagging. The work reflects the emerging challenges and opportunities presented by the ongoing progress in high-performance computing (HPC) and the deployment of the data, computational, and visualization Grids.

Analysis of tissue responses to fin tagging in Australian carcharhinids

Tissue responses to the application of Rototags and Jumbo Rototags in the first dorsal fin of Carcharhinus melanopterus, C. obscurus and C. plumbeus were examined. The acute response included tissue tearing and haemorrhage and was present by 5 days post-tagging. The intermediate response had begun by 20 days post-tagging and continued beyond 207 days. This response involved decreased red blood cell activity as the inflammatory response commenced. The chronic response had begun by 301 days and was complete by 553 days with a layer of fibrous connective tissue walling off the tag. External damage to the fin was caused by continued abrasion by the tag. Repair scales were observed at 242 days using scanning electron microscopy and were confirmed histologically in 61- and 553-day samples. Repair scales were not seen in areas of continuous abrasion. No infection was observed in tissues surrounding the wound. Disruption of the fin surface was observed due to abrasion by the tag, but did not appear to cause a severe tissue reaction. The tissue responses observed were consistent with a normal, but relatively slow, healing in the vicinity of the tag wound. Use of Rototags or Jumbo Rototags appears to be an efficient way of marking elasmobranchs with minimal damage to the shark. (C) 1998 The Fisheries Society of the British Isles.

Molecular characterization of Drosophila C virus isolates

Reverse transcription coupled with polymerase chain reaction and restriction enzyme analysis was used to characterize 12 Drosophila C virus isolates from geographically different regions. A 1.2-kb fragment was amplified from cDNA and profiles from digestion with 20 restriction enzymes were generated. Analysis of the restriction fragment data gave estimates of nucleotide divergence of 0-10% between isolates. The isolates were grouped on the basis of genetic distance estimates derived from the restriction data. For the isolates from which a single genotype could be purified, a geographical pattern in the distribution of viral genotypes was identified. The 4 Moroccan isolates were very closely related to each other, differing in only 1 restriction profile. The 2 Australian isolates were each other's closest relatives, as were the 2 isolates first recovered in France. The PCR-RFLP technique used in this study has provided us with a simple procedure which can be used to characterize DCV isolates. A single enzyme, Tag I, generated 5 distinct and diagnostic restriction fragment patterns, which allowed easy assignment of isolates to one of the five viral genotypes identified in this study. (C) 1999 Academic Press.

Molecular diversity through sugar scaffolds

Monosaccharides provide an excellent platform to tailor molecular diversity by appending desired substituents at selected positions around the sugar scaffold. The presence of five functionalized and stereo-controlled centres on the sugar scaffolds gives the chemist plenty of scope to custom design molecules to a pharmacophore model. This review focuses on the peptidomimetic developments in this area, as well as the concept of tailoring structural and functional diversity in a library using carbohydrate scaffolds and how this can lead to increased hit rates and rapid identification of leads, which has promising prospects for drug development.

Diminished CD4+/CD25+T cell and increased IFN-gamma levels occur in dogs vaccinated with Leishmune (R) in an endemic area for visceral leishmaniasis

The Leishmune (R) vaccine has been used in endemic areas to prevent canine visceral leishmaniasis in Brazil, but cytokine production induced by vaccination has rarely been investigated in dogs. This study aimed to evaluate the immune response of dogs vaccinated with Leishmune FML vaccine (Fort Dodge) against total antigen of Leishmania (Leishmania) chagasi (TAg) and FML. Twenty healthy dogs from Aracatuba, Sao Paulo, Brazil, an endemic leishmaniasis area, received three consecutive subcutaneous injection of Leishmune vaccine at 21-day intervals. PBMC were isolated before and 10 days after completing vaccination and lymphoproliferative response and antibody production against FML or total promastigote antigen were tested. Cytokines IFN-gamma, IL-4 and TNF-alpha were measured in culture supernatant and CD4+/CD25+ and CD8+/CD25+ T cell presence was determined. Analysis of the data indicated that the vaccine conferred humoral responses (100%) against both antigens and cellular immunity to FML (85%) and total antigen (80%), the supernatant of cultured cells stimulated with TAg and FML showed an increase in IFN-gamma (P < 0.05), and the vaccine reduced CD4+/CD25+ T cell presence compared to that observed before vaccination. These responses may constitute part of the immune mechanism induced by Leishmune. (C) 2010 Elsevier B.V. All rights reserved.

A low-protein, high-carbohydrate diet increases the adipose lipid content without increasing the glycerol-3-phosphate or fatty acid content in growing rats

Le taux de triacylglycerol (TAG) qui s`accumule dans le tissu adipeux depend de 2 mecanismes opposes : la lipogenese et la lipolyse. Nous avons montre anterieurement que le poids des lipides du tissu adipeux de l`epididyme (EPI) de meme que leur taux augmentent chez les rats en croissance soumis a une diete hypoproteique hyperglucidique (HPHG) pendant 15 jours. La presente etude a eu pour but d`examiner les voies impliquees dans la lipogenese et la lipolyse qui regulent l`accumulation des lipides dans le tissu. On a evalue in vivo la synthese de novo des acides gras, qui s`est revelee similaire chez les rats soumis a la diete HPHG ou a une diete temoin; toutefois, chez les rats soumis a la diete HPHG, une diminution de l`activite de la lipoproteine lipase dans le tissus adipeux de l`EPI a ete observee, ce qui laisse croire a une diminution de la capture des acides gras des lipoproteines circulantes. La diete HPHG n`a eu aucun effet sur la synthese du glycerol-3-phosphate (G3P) par la glycolyse ou la glyceroneogenese. L`activite de la glycerokinase, c.-a-d. la phosphorylation du glycerol issu de l`hydrolyse du TAG endogene pour former le GP3, n`a pas ete modifiee non plus par la diete HPHG. A l`oppose, les adipocytes des rats HPHG stimules par la norepinephrine ont eu une plus faible reponse lipolytique, meme si le taux lipolytique basal des adipocytes a ete similaire chez les 2 groupes. Ainsi, les resultats donnent a penser que la diminution de l`activite lipolytique stimulee par la norepinephrine joue un role essentiel dans l`augmentation du TAG observee dans le tissu adipeux de l`EPI des animaux HPHG, probablement en perturbant le processus d`activation de la lipolyse.

Fatty acid synthesis and generation of glycerol-3-phosphate in brown adipose tissue from rats fed a cafeteria diet

In vivo fatty acid synthesis and the pathways of glycerol-3-phosphate (G3P) production were investigated in brown adipose tissue (BAT) from rats fed a cafeteria diet for 3 weeks. In spite of BAT activation, the diet promoted an increase in the carcass fatty acid content. Plasma insulin levels were markedly increased in cafeteria diet-fed rats. Two insulin-sensitive processes, in vivo fatty acid synthesis and in vivo glucose uptake (which was used to evaluate G3P generation via glycolysis) were increased in BAT from rats fed the cafeteria diet. Direct glycerol phosphorylation, evaluated by glycerokinase (GyK) activity and incorporation of [U-(14)C]glycerol into triacylglycerol (TAG)-glycerol, was also markedly increased in BAT from these rats. In contrast, the cafeteria diet induced a marked reduction of BAT glyceroneogenesis, evaluated by phosphoenolpyruvate carboxykinase-C activity and incorporation of [1-(14)C]pyruvate into TAG-glycerol. BAT denervation resulted in an approximately 50% reduction of GyK activity, but did not significantly affect BAT in vivo fatty acid synthesis, in vivo glucose uptake, or glyceroneogenesis. The data suggest that the supply of G3P for BAT TAG synthesis can be adjusted independently from the sympathetic nervous system and solely by reciprocal changes in the generation of G3P via glycolysis and via glyceroneogenesis, with no participation of direct phosphorylation of glycerol by GyK.

Drosophila melanogaster lipins are tissue-regulated and developmentally regulated and present specific subcellular distributions

Lipins constitute a novel family of Mg2+-dependent phosphatidate phosphatases that catalyze the dephosphorylation of phosphatidic acid to yield diacylglycerol, an important intermediate in lipid metabolism and cell signaling. Whereas a single lipin is detected in less complex organisms, in mammals there are distinct lipin isoforms and paralogs that are differentially expressed among tissues. Compatible with organism tissue complexity, we show that the single Drosophila Lpin1 ortholog (CG8709, here named DmLpin) expresses at least three isoforms (DmLpinA, DmLpinK and DmLpinJ) in a temporal and spatially regulated manner. The highest levels of lipin in the fat body, where DmLpinA and DmLpinK are expressed, correlate with the highest levels of triacylglycerol (TAG) measured in this tissue. DmLpinK is the most abundant isoform in the central nervous system, where TAG levels are significantly lower than in the fat body. In the testis, where TAG levels are even lower, DmLpinJ is the predominant isoform. Together, these data suggest that DmLpinA might be the isoform that is mainly involved in TAG production, and that DmLpinK and DmLpinJ could perform other cellular functions. In addition, we demonstrate by immunofluorescence that lipins are most strongly labeled in the perinuclear region of the fat body and ventral ganglion cells. In visceral muscles of the larval midgut and adult testis, lipins present a sarcomeric distribution. In the ovary chamber, the lipin signal is concentrated in the internal rim of the ring canal. These specific subcellular localizations of the Drosophila lipins provide the basis for future investigations on putative novel cellular functions of this protein family.

Evaluation of Leptospiral Recombinant Antigens MPL17 and MPL21 for Serological Diagnosis of Leptospirosis by Enzyme-Linked Immunosorbent Assays

Leptospirosis is a zoonosis of multisystem involvement caused by pathogenic strains of the genus Leptospira. In the last few years, intensive studies aimed at the development of a vaccine have provided important knowledge about the nature of the immunological mechanisms of the host. The purpose of this study was to analyze the immune responses to two recombinant proteins, MPL17 and MPL21 (encoded by the genes LIC10765 and LIC13131, respectively) of Leptospira interrogans serovar Copenhageni in individuals during infection. The recombinant proteins were expressed in Escherichia coli as six-His tag fusion proteins and were purified from the soluble bacterial fraction by affinity chromatography with Ni2+ -charged resin. The recombinant proteins were used to evaluate their ability to bind to immunoglobulin G (IgG) (and IgG subclass) or IgM antibodies in serum samples from patients in the early and convalescent phases of leptospirosis (n = 52) by enzyme-linked immunosorbent assays. The prevalences of total IgG antibodies against MPL17 and MPL21 were 38.5% and 21.2%, respectively. The titers achieved with MPL17 were statistically significantly higher than those obtained by the reference microscopic agglutination test. The specificity of the assay was estimated to be 95.5% for MPL17 and 80.6% for MPL21 when serum samples from individuals with unrelated febrile diseases and control healthy donors were tested. The proteins are conserved among Leptospira strains that cause human and animal diseases. MPL17 and MPL21 are most likely new surface proteins of leptospires, as revealed by liquid-phase immunofluorescence assays with living organisms. Our results demonstrate that these recombinant proteins are highly immunogenic and, when they are used together, might be useful as a means of diagnosing leptospirosis.

Cyclic Fatigue Resistance of Rotary Nickel-Titanium Instruments Submitted to Nitrogen Ion Implantation

Introduction: The aim of this study was to assess cyclic fatigue resistance in rotary nickel-titanium instruments submitted to nitrogen ion implantation by using a custom-made cyclic fatigue testing apparatus. Methods: Thirty K3 files, size #25, taper 0.04, were divided into 3 experimental groups as follows: group A, 12 files exposed to nitrogen ion implantation at a dose of 2.5 x 10(17) ions/cm(2), accelerating voltage of 200 kV, currents of 1 mu A/cm(2), 130 degrees C temperature, and vacuum conditions of 10 x 10(-6) torr for 6 hours; group B, 12 nonimplanted files; and group C, 6 files submitted to thermal annealing for 6 hours at 130 degrees C. One extra file was used for process control. All files were submitted to a cyclic fatigue test that was performed with an apparatus that allowed the instruments to rotate freely, simulating rotary instrumentation of a curved canal (40-degree, 5-mm radius curve). An electric motor handpiece was used with a contra-angle of 16:1 at an operating speed of 300 rpm and a torque of 2 N-cm. Time to failure was recorded with a stopwatch in seconds and subsequently converted to number of cycles to fracture. Data were analyzed with the Student t test (P < .05). Results: Ion-implanted instruments reached significantly higher cycle numbers before fracture (mean, 510 cycles) when compared with annealed (mean, 428 cycles) and nonimplanted files (mean, 381 cycles). Conclusions: Our results showed that nitrogen ion implantation improves cyclic fatigue resistance in rotary nickel-titanium instruments. Industrial implementation. of this surface modification technique would produce rotary nickel-titanium instruments with a longer working life. (J Endod 2010;36:1183-1186)

A modified approach for vestibuloplasty in severely resorbed mandible using an implant-retained postoperative stent: a case report

Background. Severely resorbed mandibles often present a short band of keratinized tissue associated with a shallow vestibule. As a result, prominent muscle insertions are present, especially in the mental region of the mandible. This case report describes the deepening of the vestibular sulcus in an atrophic mandible by combining free gingival grafts harvested from the palate and a postoperative acrylic resin stent screwed on osseointegrated implants placed at the anterior region of the mandible. Study design. During the second-stage surgery, a split-thickness labial flap was reflected and apically sutured onto the periosteum. Two free gingival grafts were obtained and then sutured at this recipient site. A previously custom-made acrylic stent was then screwed onto the most distally positioned implants. To document the procedure`s stability over time, a metal ball was placed in the most apical part of the vestibule and standardized cephalometric radiographs were taken before and 6 months after the procedure. Linear measurements of vestibular depths over the observation time were realized using specific software for radiographic analysis. Results. The proposed technique augmented the band of attached masticatory mucosa, deepened the vestibule and prevented the muscle reinsertion. The difference between the 2 measurements of vestibular depths was 9.39 mm (initial 20.88 mm, final 11.49 mm) after a 6-month postoperative period. Conclusion. The technique, in combination with palatal mucosal graft and use of a postoperative stent, decreased the pull of mentalis muscle and provided a peri-implantally stable soft tissue around implants. (Oral Surg Oral Med Oral Pathol Oral Radiol Endod 2008; 106: e7-e14)

Mechanical Testing of Indirect Composite Materials Directly Applied on Implant Abutments

Purpose: To test the strength to failure and fracture mode of three indirect composite materials directly applied onto Ti-6Al-4V implant abutments vs cemented standard porcelain-fused-to-metal (PFM) crowns. Materials and Methods: Sixty-four locking taper abutments were randomly allocated to four groups and were cleaned in ethanol in an ultrasonic bath for 5 min. After drying under ambient conditions, the abutments were grit blasted and a custom 4-cusp molar crown mold was utilized to produce identical crowns (n = 16 per group) of Tescera (Bisco), Ceramage (Shofu), and Diamond Crown (DRM) according to the manufacturer`s instructions. The porcelain-fused-to-metal crowns were fabricated by conventional means involving the construction and a wax pattern and casting of a metallic coping followed by sintering of increasing layers of porcelain. All crowns were loaded to failure by an indenter placed at one of the cusp tips at a 1 mm/min rate. Subsequently, fracture analysis was performed by means of stereomicroscopy and scanning electron microscopy. One-way ANOVA at 95% level of significance was utilized for statistical analysis. Results: The single load to failure (+/- SD) results were: Tescera (1130 +/- 239 N), Ceramage (1099 +/- 257 N), Diamond Crown (1155 +/- 284 N), and PFM (1081 +/- 243 N). Stereomicroscopy analysis showed two distinct failure modes, where the loaded cusp failed either with or without abutment/metallic coping exposure. SEM analysis of the fractures showed multiple crack propagation towards the cervical region of the crown below a region of plastic deformation at the indenter contact region. Conclusion: The three indirect composites and PFM systems fractured at loads higher than those typically associated with normal occlusal function. Although each material had a different composition and handling technique, no significant differences were found concerning their single load to fracture resistance among composite systems and PFM.

Influence of Filling Materials on the Bonding Interface of Thin-walled Roots Reinforced with Resin and Quartz Fiber Posts

Introduction: A common complication during the restoration of severely destroyed teeth is the loss of coronal root dentine. The aim of this study was to evaluate the influence of different sealers on the bonding interface of weakened roots reinforced with resin and fiber posts. Methods: Sixty extracted maxillary canines were used. The crowns were removed, and the thickness of root dentine was reduced in the experimental (n = 40) and positive control (n = 10) groups. The specimens of experimental group were assigned to four subgroups (n = 10) according to the filling material: gutta-percha + Grossmann`s sealer, gutta-percha + AH Plus (Dentsply De Trey Gmbh, Konstanz, Germany), gutta-percha + Epiphany (Pentron Clinical Technologies, Wallingford, CT), and Resilon (Resilon Research LLC, Madison, CT) + Epiphany. In the negative control group (n = 10), canals were not filled. After post space preparation, the roots were restored with composite resin light-activated through a translucent fiber post. After 24 hours, specimens were transversally sectioned into 1-mm-thick slices. Push-out test and scanning electron microscopic (SEM) analyses of different regions were performed. Data from push-out test were analyzed by using Tukey post hoc multiple comparison tests. The percentage of failure type was calculated. Data from SEM analysis were compared by Friedman and Kruskal-Wallis tests (alpha = 0.05). Results: The mean bond strength was significantly higher in the negative control group as compared with the other groups (P < .05). In all groups, the most frequent type of failure was adhesive. Overall, apical and middle regions presented a lower density of resin tags than the coronal region (P < .05). Conclusions: The push-out bond strength was not affected by sealer or region. The canal region affected significantly the resin tag morphology and density at the bonding interface. (J Endod 2011;37:531-537)