Sequential analysis of global gene expression profiles in immature and in vitro matured bovine oocytes: potential molecular markers of oocyte maturation

Background: Without intensive selection, the majority of bovine oocytes submitted to in vitro embryo production (IVP) fail to develop to the blastocyst stage. This is attributed partly to their maturation status and competences. Using the Affymetrix GeneChip Bovine Genome Array, global mRNA expression analysis of immature (GV) and in vitro matured (IVM) bovine oocytes was carried out to characterize the transcriptome of bovine oocytes and then use a variety of approaches to determine whether the observed transcriptional changes during IVM was real or an artifact of the techniques used during analysis. Results: 8489 transcripts were detected across the two oocyte groups, of which similar to 25.0% (2117 transcripts) were differentially expressed (p < 0.001); corresponding to 589 over-expressed and 1528 under-expressed transcripts in the IVM oocytes compared to their immature counterparts. Over expression of transcripts by IVM oocytes is particularly interesting, therefore, a variety of approaches were employed to determine whether the observed transcriptional changes during IVM were real or an artifact of the techniques used during analysis, including the analysis of transcript abundance in oocytes in vitro matured in the presence of a-amanitin. Subsets of the differentially expressed genes were also validated by quantitative real-time PCR (qPCR) and the gene expression data was classified according to gene ontology and pathway enrichment. Numerous cell cycle linked (CDC2, CDK5, CDK8, HSPA2, MAPK14, TXNL4B), molecular transport (STX5, STX17, SEC22A, SEC22B), and differentiation (NACA) related genes were found to be among the several over-expressed transcripts in GV oocytes compared to the matured counterparts, while ANXA1, PLAU, STC1and LUM were among the over-expressed genes after oocyte maturation. Conclusion: Using sequential experiments, we have shown and confirmed transcriptional changes during oocyte maturation. This dataset provides a unique reference resource for studies concerned with the molecular mechanisms controlling oocyte meiotic maturation in cattle, addresses the existing conflicting issue of transcription during meiotic maturation and contributes to the global goal of improving assisted reproductive technology.

Gene Expression Complex Networks: Synthesis, Identification, and Analysis

Thanks to recent advances in molecular biology, allied to an ever increasing amount of experimental data, the functional state of thousands of genes can now be extracted simultaneously by using methods such as cDNA microarrays and RNA-Seq. Particularly important related investigations are the modeling and identification of gene regulatory networks from expression data sets. Such a knowledge is fundamental for many applications, such as disease treatment, therapeutic intervention strategies and drugs design, as well as for planning high-throughput new experiments. Methods have been developed for gene networks modeling and identification from expression profiles. However, an important open problem regards how to validate such approaches and its results. This work presents an objective approach for validation of gene network modeling and identification which comprises the following three main aspects: (1) Artificial Gene Networks (AGNs) model generation through theoretical models of complex networks, which is used to simulate temporal expression data; (2) a computational method for gene network identification from the simulated data, which is founded on a feature selection approach where a target gene is fixed and the expression profile is observed for all other genes in order to identify a relevant subset of predictors; and (3) validation of the identified AGN-based network through comparison with the original network. The proposed framework allows several types of AGNs to be generated and used in order to simulate temporal expression data. The results of the network identification method can then be compared to the original network in order to estimate its properties and accuracy. Some of the most important theoretical models of complex networks have been assessed: the uniformly-random Erdos-Renyi (ER), the small-world Watts-Strogatz (WS), the scale-free Barabasi-Albert (BA), and geographical networks (GG). The experimental results indicate that the inference method was sensitive to average degree k variation, decreasing its network recovery rate with the increase of k. The signal size was important for the inference method to get better accuracy in the network identification rate, presenting very good results with small expression profiles. However, the adopted inference method was not sensible to recognize distinct structures of interaction among genes, presenting a similar behavior when applied to different network topologies. In summary, the proposed framework, though simple, was adequate for the validation of the inferred networks by identifying some properties of the evaluated method, which can be extended to other inference methods.

KeaA, a Dictyostelium kelch-domain protein that regulates the response to stress and development

Background: The protein kinase YakA is responsible for the growth arrest and induction of developmental processes that occur upon starvation of Dictyostelium cells. yakA-cells are aggregation deficient, have a faster cell cycle and are hypersensitive to oxidative and nitrosoative stress. With the aim of isolating members of the YakA pathway, suppressors of the death induced by nitrosoative stress in the yakA-cells were identified. One of the suppressor mutations occurred in keaA, a gene identical to DG1106 and similar to Keap1 from mice and the Kelch protein from Drosophila, among others that contain Kelch domains. Results: A mutation in keaA suppresses the hypersensitivity to oxidative and nitrosoative stresses but not the faster growth phenotype of yakA-cells. The growth profile of keaA deficient cells indicates that this gene is necessary for growth. keaA deficient cells are more resistant to nitrosoative and oxidative stress and keaA is necessary for the production and detection of cAMP. A morphological analysis of keaA deficient cells during multicellular development indicated that, although the mutant is not absolutely deficient in aggregation, cells do not efficiently participate in the process. Gene expression analysis using cDNA microarrays of wild-type and keaA deficient cells indicated a role for KeaA in the regulation of the cell cycle and pre-starvation responses. Conclusions: KeaA is required for cAMP signaling following stress. Our studies indicate a role for kelch proteins in the signaling that regulates the cell cycle and development in response to changes in the environmental conditions.

Structure-Function Analysis of the HrpB2-HrcU Interaction in the Xanthomonas citri Type III Secretion System

Bacterial type III secretion systems deliver protein virulence factors to host cells. Here we characterize the interaction between HrpB2, a small protein secreted by the Xanthomonas citri subsp. citri type III secretion system, and the cytosolic domain of the inner membrane protein HrcU, a paralog of the flagellar protein FlhB. We show that a recombinant fragment corresponding to the C-terminal cytosolic domain of HrcU produced in E. coli suffers cleavage within a conserved Asn264-Pro265-Thr266-His267 (NPTH) sequence. A recombinant HrcU cytosolic domain with N264A, P265A, T266A mutations at the cleavage site (HrcU(AAAH)) was not cleaved and interacted with HrpB2. Furthermore, a polypeptide corresponding to the sequence following the NPTH cleavage site also interacted with HrpB2 indicating that the site for interaction is located after the NPTH site. Non-polar deletion mutants of the hrcU and hrpB2 genes resulted in a total loss of pathogenicity in susceptible citrus plants and disease symptoms could be recovered by expression of HrpB2 and HrcU from extrachromossomal plasmids. Complementation of the Delta hrcU mutant with HrcU(AAAH) produced canker lesions similar to those observed when complemented with wild-type HrcU. HrpB2 secretion however, was significantly reduced in the Delta hrcU mutant complemented with HrcU(AAAH), suggesting that an intact and cleavable NPTH site in HrcU is necessary for total functionally of T3SS in X. citri subsp. citri. Complementation of the Delta hrpB2 X. citri subsp. citri strain with a series of hrpB2 gene mutants revealed that the highly conserved HrpB2 C-terminus is essential for T3SS-dependent development of citrus canker symptoms in planta.

New genes of Xanthomonas citri subsp citri involved in pathogenesis and adaptation revealed by a transposon-based mutant library

Background: Citrus canker is a disease caused by the phytopathogens Xanthomonas citri subsp. citri, Xanthomonas fuscans subsp. aurantifolli and Xanthomonas alfalfae subsp. citrumelonis. The first of the three species, which causes citrus bacterial canker type A, is the most widely spread and severe, attacking all citrus species. In Brazil, this species is the most important, being found in practically all areas where citrus canker has been detected. Like most phytobacterioses, there is no efficient way to control citrus canker. Considering the importance of the disease worldwide, investigation is needed to accurately detect which genes are related to the pathogen-host adaptation process and which are associated with pathogenesis. Results: Through transposon insertion mutagenesis, 10,000 mutants of Xanthomonas citri subsp. citri strain 306 (Xcc) were obtained, and 3,300 were inoculated in Rangpur lime (Citrus limonia) leaves. Their ability to cause citrus canker was analyzed every 3 days until 21 days after inoculation; a set of 44 mutants showed altered virulence, with 8 presenting a complete loss of causing citrus canker symptoms. Sequencing of the insertion site in all 44 mutants revealed that 35 different ORFs were hit, since some ORFs were hit in more than one mutant, with mutants for the same ORF presenting the same phenotype. An analysis of these ORFs showed that some encoded genes were previously known as related to pathogenicity in phytobacteria and, more interestingly, revealed new genes never implicated with Xanthomonas pathogenicity before, including hypothetical ORFs. Among the 8 mutants with no canker symptoms are the hrpB4 and hrpX genes, two genes that belong to type III secretion system (TTSS), two hypothetical ORFS and, surprisingly, the htrA gene, a gene reported as involved with the virulence process in animal-pathogenic bacteria but not described as involved in phytobacteria virulence. Nucleic acid hybridization using labeled cDNA probes showed that some of the mutated genes are differentially expressed when the bacterium is grown in citrus leaves. Finally, comparative genomic analysis revealed that 5 mutated ORFs are in new putative pathogenicity islands. Conclusion: The identification of these new genes related with Xcc infection and virulence is a great step towards the understanding of plant-pathogen interactions and could allow the development of strategies to control citrus canker.

Ethanol production process from banana fruit and its lignocellulosic residues: Energy analysis

Tropical countries, such as Brazil and Colombia, have the possibility of using agricultural lands for growing biomass to produce bio-fuels such as biodiesel and ethanol. This study applies an energy analysis to the production process of anhydrous ethanol obtained from the hydrolysis of starch and cellulosic and hemicellulosic material present in the banana fruit and its residual biomass. Four different production routes were analyzed: acid hydrolysis of amylaceous material (banana pulp and banana fruit) and enzymatic hydrolysis of lignocellulosic material (flower stalk and banana skin). The analysis considered banana plant cultivation, feedstock transport, hydrolysis, fermentation, distillation, dehydration, residue treatment and utility plant. The best indexes were obtained for amylaceous material for which mass performance varied from 346.5 L/t to 388.7 L/t, Net Energy Value (NEV) ranged from 9.86 MJ/L to 9.94 MJ/L and the energy ratio was 1.9 MJ/MJ. For lignocellulosic materials, the figures were less favorable: mass performance varied from 86.1 to 123.5 L/t, NEV from 5.24 10 8.79 MJ/L and energy ratio from 1.3 to 1.6 MJ/MJ. The analysis showed, however, that both processes can be considered energetically feasible. (C) 2010 Elsevier Ltd. All rights reserved.

An air-standard cycle and a thermodynamic perspective on operational limits of Ranque-Hilsh or vortex tubes

A Thermodynamic air-standard cycle was envisaged for Ranque-Hilsh (R-H) or Vortex Tubes to provide relevant Thermodynamic analysis and tools for setting operating limits according to the conservation laws of mass and energy, as well as the constraint of the Second Law of Thermodynamics. The study used an integral or control volume approach and resulted in establishing working equations for evaluating the performance of an R-H tube. The work proved that the coefficient of performance does not depend on the R-H tube operating mode, i.e., the same value is obtained independently if the R-H tube operates either as a heat pump or as a refrigeration device. It was also shown that the isentropic coefficient of performance displays optima values of cold and hot mass fractions for a given operating pressure ratio. Finally, the study was concluded by comparing the present analysis with some experimental data available in the literature for operating pressures ranging 2-11 atm. (C) 2010 Elsevier Ltd and IIR. All rights reserved.

Exergy and thermoeconomic analysis of a turbofan engine during a typical commercial flight

In an energy perspective of cost-reduction and configuration-optimization, it becomes necessary to develop and use advanced tools for the analysis, design and improvement of energy conversion systems. In the aeronautical industry, such trend is fundamental since this industry has evolved to design extremely complex aircrafts, with highly integrated systems, requiring more information in order to evaluate the whole system. The aim of this paper is to present an exergy-based analysis as to evaluate the global performance of a typical turbofan engine and its components. The study presents values for exergy efficiency over the whole flight cycle, critical equipment and flight phases considering exergy destruction and estimating internal and exhaust flow costs. (C) 2009 Elsevier Ltd. All rights reserved.

Reliability Analysis in Reciprocating Compressors for Refrigeration Systems

The most-used refrigeration system is the vapor-compression system. In this cycle, the compressor is the most complex and expensive component, especially the reciprocating semihermetic type, which is often used in food product conservation. This component is very sensitive to variations in its operating conditions. If these conditions reach unacceptable levels, failures are practically inevitable. Therefore, maintenance actions should be taken in order to maintain good performance of such compressors and to avoid undesirable stops of the system. To achieve such a goal, one has to evaluate the reliability of the system and/or the components. In this case, reliability means the probability that some equipment cannot perform their requested functions for an established time period, under defined operating conditions. One of the tools used to improve component reliability is the failure mode and effect analysis (FMEA). This paper proposes that the methodology of FMEA be used as a tool to evaluate the main failures found in semihermetic reciprocating compressors used in refrigeration systems. Based on the results, some suggestions for maintenance are addressed.

Exergy-based method for analyzing the composition of the electricity cost generated in gas-fired combined cycle plants

The proposed method to analyze the composition of the cost of electricity is based on the energy conversion processes and the destruction of the exergy through the several thermodynamic processes that comprise a combined cycle power plant. The method uses thermoeconomics to evaluate and allocate the cost of exergy throughout the processes, considering costs related to inputs and investment in equipment. Although the concept may be applied to any combined cycle or cogeneration plant, this work develops only the mathematical modeling for three-pressure heat recovery steam generator (HRSG) configurations and total condensation of the produced steam. It is possible to study any n x 1 plant configuration (n sets of gas turbine and HRSGs associated to one steam turbine generator and condenser) with the developed model, assuming that every train operates identically and in steady state. The presented model was conceived from a complex configuration of a real power plant, over which variations may be applied in order to adapt it to a defined configuration under study [Borelli SJS. Method for the analysis of the composition of electricity costs in combined cycle thermoelectric power plants. Master in Energy Dissertation, Interdisciplinary Program of Energy, Institute of Eletro-technical and Energy, University of Sao Paulo, Sao Paulo, Brazil, 2005 (in Portuguese)]. The variations and adaptations include, for instance, use of reheat, supplementary firing and partial load operation. It is also possible to undertake sensitivity analysis on geometrical equipment parameters. (C) 2007 Elsevier Ltd. All rights reserved.

Availability analysis of heat recovery steam generators used in thermal power plants

The combined-cycle gas and steam turbine power plant presents three main pieces of equipment: gas turbines, steam turbines and heat recovery steam generator (HRSG). In case of HRSG failure the steam cycle is shut down, reducing the power plant output. Considering that the technology for design, construction and operation of high capacity HRSGs is quite recent its availability should be carefully evaluated in order to foresee the performance of the power plant. This study presents a method for reliability and availability evaluation of HRSGs installed in combined-cycle power plant. The method`s first step consists in the elaboration of the steam generator functional tree and development of failure mode and effects analysis. The next step involves a reliability and availability analysis based on the time to failure and time to repair data recorded during the steam generator operation. The third step, aiming at availability improvement, recommends the fault-tree analysis development to identify components the failure (or combination of failures) of which can cause the HRSG shutdown. Those components maintenance policy can be improved through the use of reliability centered maintenance (RCM) concepts. The method is applied on the analysis of two HRSGs installed in a 500 MW combined-cycle power plant. (C) 2010 Elsevier Ltd. All rights reserved.

Fretting fatigue in overhead conductors: Rig design and failure analysis of a Grosbeak aluminium cable steel reinforced conductor

The performance optimisation of overhead conductors depends on the systematic investigation of the fretting fatigue mechanisms in the conductor/clamping system. As a consequence, a fretting fatigue rig was designed and a limited range of fatigue tests was carried out at the middle high cycle fatigue regime in order to access an exploratory S-N curve for a Grosbeak conductor, which was mounted on a mono-articulated aluminium clamping system. Subsequent to these preliminary fatigue tests, the components of the conductor/clamping system, such as ACSR conductor, upper and lower clamps, bolt and nuts, were subjected to a failure analysis procedure in order to investigate the metallurgical free variables interfering on the fatigue test results, aiming at the optimisation of the testing reproducibility. The results indicated that the rupture of the planar fracture surfaces observed in the external At strands of the conductor tested under lower bending amplitude (0.9 mm) occurred by fatigue cracking (I mm deep), followed by shear overload. The V-type fracture surfaces observed in some At strands of the conductor tested under higher bending amplitude (1.3 mm) were also produced by fatigue cracking (approximately 400 mu m deep), followed by shear overload. Shear overload fracture (45 degrees fracture surface) was also observed on the remaining At wires of the conductor tested under higher bending amplitude (1.3 mm). Additionally, the upper and lower Al-cast clamps presented microstructure-sensitive cracking, which was folowed by particle detachment and formation of abrasive debris on the clamp/conductor tribo-interface, promoting even further the fretting mechanism. The detrimental formation of abrasive debris might be inhibited by the selection of a more suitable class of as-cast At alloy for the production of clamps. Finally, the bolt/nut system showed intense degradation of the carbon steel nut (fabricated in ferritic-pearlitic carbon steel, featuring machined threads with 190 HV), with intense plastic deformation and loss of material. Proper selection of both the bolt and nut materials and the finishing processing might prevent the loss in the clamping pressure during the fretting testing. It is important to control the specification of these components (clamps, bolt and nuts) prior to the start of large scale fretting fatigue testing of the overhead conductors in order to increase the reproducibility of this assessment. (c) 2008 Elsevier Ltd. All rights reserved.

Cloning, expression, molecular modelling and docking analysis of glutathione transferase from Saccharum officinarum

Sugarcane yield and quality are affected by a number of biotic and abiotic stresses. In response to such stresses, plants may increase the activities of some enzymes such as glutathione transferase (GST), which are involved in the detoxification of xenobiotics. Thus, a sugarcane GST was modelled and molecular docked using the program LIGIN to investigate the contributions of the active site residues towards the binding of reduced glutathione (GSH) and 1-chloro-2,4-dinitrobenzene (CDNB). As a result, W13 and I119 were identified as key residues for the specificity of sugarcane GSTF1 (SoGSTF1) towards CDNB. To obtain a better understanding of the catalytic specificity of sugarcane GST (SoGSTF1), two mutants were designed, W13L and I119F. Tertiary structure models and the same docking procedure were performed to explain the interactions between sugarcane GSTs with GSH and CDNB. An electron-sharing network for GSH interaction was also proposed. The SoGSTF1 and the mutated gene constructions were cloned and expressed in Escherichia coli and the expressed protein purified. Kinetic analyses revealed different Km values not only for CDNB, but also for GSH. The Km values were 0.2, 1.3 and 0.3 mM for GSH, and 0.9, 1.2 and 0.5 mM for CDNB, for the wild type, W13L mutant and I119F mutant, respectively. The V(max) values were 297.6, 224.5 and 171.8 mu mol min(-1) mg(-1) protein for GSH, and 372.3, 170.6 and 160.4 mu mol min(-1) mg(-1) protein for CDNB.

Analysis of genomic and functional RFLP derived markers associated with sucrose content, fiber and yield QTLs in a sugarcane (Saccharum spp.) commercial cross

Expressed sequence tags derived markers have a great potential to be used in functional map construction and QTL tagging. In the present work, sugarcane genomic probes and expressed sequence tags having homology to genes, mostly involved in carbohydrate metabolism were used in RFLP assays to identify putative QTLs as well as their epistatic interactions for fiber content, cane yield, pol and tones of sugar per hectare, at two crop cycles in a progeny derived from a bi-parental cross of sugarcane elite materials. A hundred and twenty marker trait associations were found, of which 26 at both crop cycle and 32 only at first ratoon cane. A sucrose synthase derived marker was associated with a putative QTL having a high negative effect on cane yield and also with a QTL having a positive effect on Pol at both crop cycles. Fifty digenic epistatic marker interactions were identified for the four traits evaluated. Of these, only two were observed at both crop cycles.

Cloning, characterization and functional analysis of a 1-FEH cDNA from Vernonia herbacea (Vell.) Rusby

Variations in the inulin contents have been detected in rhizophores of Vernonia herbacea during the phenological cycle. These variations indicate the occurrence of active inulin synthesis and depolymerization throughout the cycle and a role for this carbohydrate as a reserve compound. 1-Fructan exohydrolase (1-FEH) is the enzyme responsible for inulin depolymerization, and its activity has been detected in rhizophores of sprouting plants. Defoliation and low temperature are enhancer conditions of this 1-FEH activity. The aim of the present work was the cloning of this enzyme. Rhizophores were collected from plants induced to sprout, followed by storage at 5C. A full length 1-FEH cDNA sequence was obtained by PCR and inverse PCR techniques, and expressed in Pichia pastoris. Cold storage enhances FEH gene expression. Vh1-FEH was shown to be a functional 1-FEH, hydrolyzing predominantly -2,1 linkages, sharing high identity with chicory FEH sequences, and its activity was inhibited by 81 in the presence of 10 mM sucrose. In V. herbacea, low temperature and sucrose play a role in the control of fructan degradation. This is the first study concerning the cloning and functional analysis of a 1-FEH cDNA of a native species from the Brazilian Cerrado. Results will contribute to understanding the role of fructans in the establishment of a very successful fructan flora of the Brazilian Cerrado, subjected to water limitation and low temperature during winter.