Production of DNA microarray and expression analysis of genes from Xylella fastidiosa in different culture media

DNA Microarray was developed to monitor the expression of many genes from Xylella fastidiosa, allowing the side by-side comparison of two situations in a single experiment. The experiments were performed using X. fastidiosa cells grown in two culture media: BCYE and XDM2. The primers were synthesized, spotted onto glass slides and the array was hybridized against fluorescently labeled cDNAs. The emitted signals were quantified, normalized and the data were statistically analyzed to verify the differentially expressed genes. According to the data, 104 genes were differentially expressed in XDM2 and 30 genes in BCYE media. The present study showed that DNA microarray technique efficiently differentiate the expressed genes under different conditions.

Eletroforese capilar acoplada à espectrometria de massas (CE-MS): vinte anos de desenvolvimento

CE-MS has been increasingly used for analysis of a vast array of compounds. This article reviews the different electrophoretic modes, interfaces and mass analyzers that are commonly used in the CE-MS coupling, as well as the technique advantages and performance characteristics. A large compilation of CE-MS applications is also presented. Therefore, this review is both a guide for beginners and a collection of key references for people who are familiar to the technique. Furthermore, this is the first CE-MS review published in a Brazilian journal and marks the installation of the first two commercial CE-MS units in Sao Paulo State.

Métodos para fabricação de microeletrodos visando a detecção em microambientes

Analysis at microenvironments, like single cells or in minute volumes (nL), is an area of great interest for analytical and biological sciences. Measurements at these experimental conditions demand analytical tools (microelectrodes) capable of monitoring with rapid response, good resolution and minimal perturbation of the system. The major drawbacks in producing these microscopic electrodes have been largely overcome, principally due to the development of new fabrication methods. In this review, these procedures are described with emphasis to those devoted to the construction of microelectrodes for application in microenvironments. Examples of our efforts to use these devices as effective electrochemical sensors are also addressed.

A novel disposable electrochemical microcell: construction and characterization

An alternative technique for the fabrication of disposable electrochemical microcells containing working, reference and auxiliary electrodes on a single device is reported. The procedure is based on thermal-transfer of toner masks onto CD-R (recordable compact discs) gold surfaces to define the layout of the electrodes (contour). In a subsequent step, the layout is manually painted with a permanent marker pen. The unprotected gold surface is conveniently etched (chemical corrosion) and the ink is then easily removed with ethanol, generating gold surfaces without contamination. The final and reproducible area of the electrodes is defined by heat transference of a second toner mask. Silver epoxy is deposited on one of the gold bands which is the satisfactorily used as reference electrode. These microcells were electrochemically characterized by cyclic, linear, and square wave voltammetry, and several electroactive species were used as model systems. The area reproducibility of the electrodes for different microcells was studied and a relative standard deviation better than 1,0% (n = 10) was obtained. Disposable electrochemical microcells were successfully used in analysis of liquid samples with volumes lower than 200 µL and good stability and reproducibility (RSD less than 2.0%) were achieved. These microcells were also evaluated for quantification of paracetamol and dipyrone in pharmaceutical formulations.

Novos táxons e novo registro em Hemilophini (Coleoptera: Cerambycidae: Lamiinae)

Novas espécies descritas e ilustradas: Adesmus nigrolineatus sp. nov. do México (Oaxaca). Da Costa Rica: A. moruna sp. nov. (Heredia); Corcovado bezarki sp. nov. (Guanacaste); Alampyris fuscus sp. nov. (Guanacaste), Cariua gen. nov. espécie-tipo C. sulphurea sp. nov., (Guanacaste). Da Bolívia: Phoebemima albomaculata sp. nov. (Cochabamba); Ipepo gen. nov. espécie-tipo I. dilatatus sp. nov. (Santa Cruz). Do Brasil: Adesmus facetus sp. nov. e Canarana arguta sp. nov. (Rondônia). É acrescentado novo registro na Costa Rica para Piruanycha pitilla Galileo & Martins, 2005. As três espécies novas de Adesmus distinguem-se: A. nigrolineatus sp. nov. pelas faixas longitudinais de tegumento preto nos élitros; A. moruna sp. nov. pelos élitros inteiramente pretos; A. facetus pelas faixas oblíquas de pubescência branca após o meio dos élitros além das manchas do quarto apical e das epipleuras. Phoebemima albomaculata sp. nov. caracteriza-se pela mancha basal de pubescência branca dos élitros estendendo-se sobre a sutura. Corcovado bezarki sp. nov. distingue-se pelo escapo preto e antenômeros esbranquiçados. Canarana arguta sp. nov. tem o protórax e os urosternitos I a IV cobertos por densa pubescência amarelada. Alampyris fusca sp. nov. difere de A. cretaria principalmente pelo antenômero III mais longo que o escapo. Cariua sulphurea sp. nov. separa-se pela presença de urosternitos revestidos por pubescência branca compacta e Ipepo dilatatus sp. nov. caracteriza-se pelos élitros tri-carenados.

Dietas com nitrogênio não-proteico para fêmeas bovinas superovuladas sem prévia adaptação durante curto tempo e em diferentes fases do ciclo estral

Objetivou-se neste estudo avaliar o efeito do fornecimento, sem prévia adaptação, durante curto tempo e em diferentes fases do ciclo estral, de dietas contendo nitrogênio não-proteico (NNP) na produção, na qualidade e no grau de desenvolvimento de embriões recuperados em fêmeas bovinas superovuladas. Sessenta e oito vacas Nelore foram distribuídas em três grupos: um controle e dois com fornecimento de ureia antes (UA = do dia -5 ao dia 0) e após (UD = dia 0 ao dia 5) a inseminação artificial. As vacas foram mantidas em pastagem e receberam concentrado (3,0 kg/animal/dia) durante 16 dias. Foram formulados dois concentrados, e as dietas totais (concentrado e consumo estimado de pastagem) apresentaram 12,0% (dieta controle) e 14,6% (dieta NNP) de proteína bruta (PB). As vacas foram sincronizadas, superovuladas e inseminadas. Sete dias (dia 7) após a inseminação (dia 0), realizou-se a colheita e análise dos embriões. Amostras de sangue foram coletadas nos dias -5, 0 e 5 para determinação da concentração de nitrogênio ureico plasmático (NUP), glicose, insulina e progesterona. A época de fornecimento de ureia influenciou as concentrações médias de NUP nos dias -5, 0 e 5, mas não tiveram efeito nas concentrações de glicose, insulina e progesterona. O período de fornecimento da ureia teve efeito na porcentagem de mórulas compactas em relação ao total de estruturas (UA = 51,4 vs. UD = 15,3%), em relação ao total de oócitos fecundados (UA = 62,5 vs. UD = 30,6%) e em relação ao total de embriões viáveis (UA = 68,8 vs. UD = 38,6%). No grupo que recebeu ureia depois da inseminação artificial, houve redução de 70,2% da proporção de mórulas compactas por total de estruturas em relação ao grupo que recebeu ureia antes da inseminação. Dietas com nitrogênio não-proteico fornecidas imediatamente após a inseminação promovem aceleração do desenvolvimento embrionário inicial.

An Environmental Friendly Procedure for Photometric Determination of Hypochlorite in Tap Water Employing a Miniaturized Multicommuted Flow Analysis Setup

A photometric procedure for the determination of ClO(-) in tap water employing a miniaturized multicommuted flow analysis setup and an LED-based photometer is described. The analytical procedure was implemented using leucocrystal violet (LCV; 4,4', 4 ''-methylidynetris (N, N-dimethylaniline), C(25)H(31)N(3)) as a chromogenic reagent. Solenoid micropumps employed for solutions propelling were assembled together with the photometer in order to compose a compact unit of small dimensions. After control variables optimization, the system was applied for the determination of ClO(-) in samples of tap water, and aiming accuracy assessment samples were also analyzed using an independent method. Applying the paired t-test between results obtained using both methods, no significant difference at the 95% confidence level was observed. Other useful features include low reagent consumption, 2.4 mu g of LCV per determination, a linear response ranging from 0.02 up to 2.0 mg L(-1) ClO(-), a relative standard deviation of 1.0% (n = 11) for samples containing 0.2 mg L(-1) ClO(-), a detection limit of 6.0 mu g L(-1) ClO(-), a sampling throughput of 84 determinations per hour, and a waste generation of 432 mu L per determination.

Free expanding cloud of cold atoms as an atomic standard: Ramsey fringes contrast

A compact frequency standard based on an expanding cold (133)CS cloud is under development in our laboratory. In a first experiment, Cs cold atoms were prepared by a magneto-optical trap in a vapor cell, and a microwave antenna was used to transmit the radiation for the clock transition. The signal obtained from fluorescence of the expanding cold atoms cloud is used to lock a microwave chain. In this way the overall system stability is evaluated. A theoretical model based on a two-level system interacting with the two microwave pulses enables interpretation for the observed features, especially the poor Ramsey fringes contrast. (C) 2008 Optical Society of America.

AVERAGE CONTINUOUS CONTROL OF PIECEWISE DETERMINISTIC MARKOV PROCESSES

This paper deals with the long run average continuous control problem of piecewise deterministic Markov processes (PDMPs) taking values in a general Borel space and with compact action space depending on the state variable. The control variable acts on the jump rate and transition measure of the PDMP, and the running and boundary costs are assumed to be positive but not necessarily bounded. Our first main result is to obtain an optimality equation for the long run average cost in terms of a discrete-time optimality equation related to the embedded Markov chain given by the postjump location of the PDMP. Our second main result guarantees the existence of a feedback measurable selector for the discrete-time optimality equation by establishing a connection between this equation and an integro-differential equation. Our final main result is to obtain some sufficient conditions for the existence of a solution for a discrete-time optimality inequality and an ordinary optimal feedback control for the long run average cost using the so-called vanishing discount approach. Two examples are presented illustrating the possible applications of the results developed in the paper.

Chicken skeletal muscle-associated macroarray for gene discovery

Macro- and microarrays are well-established technologies to determine gene functions through repeated measurements of transcript abundance. We constructed a chicken skeletal muscle-associated array based on a muscle-specific EST database, which was used to generate a tissue expression dataset of similar to 4500 chicken genes across 5 adult tissues (skeletal muscle, heart, liver, brain, and skin). Only a small number of ESTs were sufficiently well characterized by BLAST searches to determine their probable cellular functions. Evidence of a particular tissue-characteristic expression can be considered an indication that the transcript is likely to be functionally significant. The skeletal muscle macroarray platform was first used to search for evidence of tissue-specific expression, focusing on the biological function of genes/transcripts, since gene expression profiles generated across tissues were found to be reliable and consistent. Hierarchical clustering analysis revealed consistent clustering among genes assigned to 'developmental growth', such as the ontology genes and germ layers. Accuracy of the expression data was supported by comparing information from known transcripts and tissue from which the transcript was derived with macroarray data. Hybridization assays resulted in consistent tissue expression profile, which will be useful to dissect tissue-regulatory networks and to predict functions of novel genes identified after extensive sequencing of the genomes of model organisms. Screening our skeletal-muscle platform using 5 chicken adult tissues allowed us identifying 43 'tissue-specific' transcripts, and 112 co-expressed uncharacterized transcripts with 62 putative motifs. This platform also represents an important tool for functional investigation of novel genes; to determine expression pattern according to developmental stages; to evaluate differences in muscular growth potential between chicken lines, and to identify tissue-specific genes.

High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species

Background: High-throughput SNP genotyping has become an essential requirement for molecular breeding and population genomics studies in plant species. Large scale SNP developments have been reported for several mainstream crops. A growing interest now exists to expand the speed and resolution of genetic analysis to outbred species with highly heterozygous genomes. When nucleotide diversity is high, a refined diagnosis of the target SNP sequence context is needed to convert queried SNPs into high-quality genotypes using the Golden Gate Genotyping Technology (GGGT). This issue becomes exacerbated when attempting to transfer SNPs across species, a scarcely explored topic in plants, and likely to become significant for population genomics and inter specific breeding applications in less domesticated and less funded plant genera. Results: We have successfully developed the first set of 768 SNPs assayed by the GGGT for the highly heterozygous genome of Eucalyptus from a mixed Sanger/454 database with 1,164,695 ESTs and the preliminary 4.5X draft genome sequence for E. grandis. A systematic assessment of in silico SNP filtering requirements showed that stringent constraints on the SNP surrounding sequences have a significant impact on SNP genotyping performance and polymorphism. SNP assay success was high for the 288 SNPs selected with more rigorous in silico constraints; 93% of them provided high quality genotype calls and 71% of them were polymorphic in a diverse panel of 96 individuals of five different species. SNP reliability was high across nine Eucalyptus species belonging to three sections within subgenus Symphomyrtus and still satisfactory across species of two additional subgenera, although polymorphism declined as phylogenetic distance increased. Conclusions: This study indicates that the GGGT performs well both within and across species of Eucalyptus notwithstanding its nucleotide diversity >= 2%. The development of a much larger array of informative SNPs across multiple Eucalyptus species is feasible, although strongly dependent on having a representative and sufficiently deep collection of sequences from many individuals of each target species. A higher density SNP platform will be instrumental to undertake genome-wide phylogenetic and population genomics studies and to implement molecular breeding by Genomic Selection in Eucalyptus.

Cyclooligomerisation of azido-alkyne-functionalised sugars: synthesis of 1,6-linked cyclic pseudo-galactooligosaccharides and assessment of their sialylation by Trypanosoma cruzi trans-sialidase

Cyclic pseudo-galactooligosaccharides were synthesized by cyclooligomerisation of isomeric azido-alkyne derivatives of beta-D-galactopyranose under Cu(I)-catalysed azide-alkyne 1,3-dipolar cycloaddition reaction conditions. The principal products isolated were cyclic dimers and trimers, with lower amounts of cyclic tetramer and pentamer also evident in some cases. Molecular mechanics calculations suggest very compact but flexible structures for the cyclic trimers, with secondary OH groups exposed outside the macrocycle and available for enzymatic glycosylation. The cyclic dimers and trimers represent a new type of acceptor substrate for Trypanosoma cruzi trans-sialidase, giving rise to doubly and triply sialylated glycomacrocycles, respectively.

State-of-the-Art and Future Directions for Green Human Resource Management: Introduction to the Special Issue

The topic of environmental sustainability is generating increased concern among business executives, governments, consumers, and management scholars. As these stakeholders struggle with the challenges and opportunities presented by an array of environmental issues, HRM scholars and practitioners alike have been relatively slow to engage in the ongoing discussions and debates. Through this special issue on Green FIRM, we seek to stimulate the field of HRM to expand its role in the pursuit of environmentally sustainable business. In this introduction to the special issue, we first provide an overview of the articles that appear in the special issue. Next we present a detailed discussion of research questions that arise from a consideration of several functional HRM practices, including performance management; training, development, and learning; compensation and rewards; and organizational culture. We conclude by describing opportunities for research at the intersection of strategic HRM and environmental management. If pursued with vigor, research addressing this extensive agenda could begin to establish a healthy field of Green FIRM scholarship.

Lineage relationship of prostate cancer cell types based on gene expression

Background: Prostate tumor heterogeneity is a major factor in disease management. Heterogeneity could be due to multiple cancer cell types with distinct gene expression. Of clinical importance is the so-called cancer stem cell type. Cell type-specific transcriptomes are used to examine lineage relationship among cancer cell types and their expression similarity to normal cell types including stem/progenitor cells. Methods: Transcriptomes were determined by Affymetrix DNA array analysis for the following cell types. Putative prostate progenitor cell populations were characterized and isolated by expression of the membrane transporter ABCG2. Stem cells were represented by embryonic stem and embryonal carcinoma cells. The cancer cell types were Gleason pattern 3 (glandular histomorphology) and pattern 4 (aglandular) sorted from primary tumors, cultured prostate cancer cell lines originally established from metastatic lesions, xenografts LuCaP 35 (adenocarcinoma phenotype) and LuCaP 49 (neuroendocrine/small cell carcinoma) grown in mice. No detectable gene expression differences were detected among serial passages of the LuCaP xenografts. Results: Based on transcriptomes, the different cancer cell types could be clustered into a luminal-like grouping and a non-luminal-like (also not basal-like) grouping. The non-luminal-like types showed expression more similar to that of stem/progenitor cells than the luminal-like types. However, none showed expression of stem cell genes known to maintain stemness. Conclusions: Non-luminal-like types are all representatives of aggressive disease, and this could be attributed to the similarity in overall gene expression to stem and progenitor cell types.

Gene expression relationship between prostate cancer cells of Gleason 3, 4 and normal epithelial cells as revealed by cell type-specific transcriptomes

Background: Prostate cancer cells in primary tumors have been typed CD10(-)/CD13(-)/CD24(hi)/CD26(+)/CD38(lo)/CD44(-)/CD104(-). This CD phenotype suggests a lineage relationship between cancer cells and luminal cells. The Gleason grade of tumors is a descriptive of tumor glandular differentiation. Higher Gleason scores are associated with treatment failure. Methods: CD26(+) cancer cells were isolated from Gleason 3+3 (G3) and Gleason 4+4 (G4) tumors by cell sorting, and their gene expression or transcriptome was determined by Affymetrix DNA array analysis. Dataset analysis was used to determine gene expression similarities and differences between G3 and G4 as well as to prostate cancer cell lines and histologically normal prostate luminal cells. Results: The G3 and G4 transcriptomes were compared to those of prostatic cell types of non-cancer, which included luminal, basal, stromal fibromuscular, and endothelial. A principal components analysis of the various transcriptome datasets indicated a closer relationship between luminal and G3 than luminal and G4. Dataset comparison also showed that the cancer transcriptomes differed substantially from those of prostate cancer cell lines. Conclusions: Genes differentially expressed in cancer are potential biomarkers for cancer detection, and those differentially expressed between G3 and G4 are potential biomarkers for disease stratification given that G4 cancer is associated with poor outcomes. Differentially expressed genes likely contribute to the prostate cancer phenotype and constitute the signatures of these particular cancer cell types.