Untersuchungen zur Eliminierung und Resorption von Zink aus Säugerspermatozoen während der Nebenhodenpassage

Während der Spermatogenese wird das Element Zink an die Sulfhydrylreste der Cysteine in den Mantelfaserproteinen der Spermienflagellen gebunden. So kann in den noch unreifen Mantelfasern die ungerichtete Ausbildung von Disulfidbrücken verhindert werden. Im Zuge der Spermatozoenreifung während der Nebenhodenpassage wird dieses Zink androgenabhängig zu einem hohen Prozentsatz wieder eliminiert. Die nun gerichtete Ausbildung von Disulfidbrücken ermöglicht die Versteifung der Mantelfasern. Diese Rigidität stellt die Voraussetzung zur progressiven Motilität dar, ohne die eine Fertilisierung der Eizelle im weiblichen Genitaltrakt nicht möglich ist. Da eine negative Korrelation zwischen dem Zinkgehalt von Flagellen und ihrer Motilität besteht (Henkel et al., 1999), hat die Zinkeliminierung während der Nebenhodenpassage eine entscheidende Bedeutung in der Entwicklung der Spermatozoen. Die vorliegende Arbeit untersucht die Mechanismen der epididymalen Zinkeliminierung sowie die an diesem Prozess beteiligten Komponenten und den Verbleib des eliminierten Zinks am System des Bullen, der Ratte und des Menschen. Mittels proteinchemischer Verfahren kann im bovinen System ein zinkbindendes 60 kDa-Protein als Albumin identifiziert werden. Ein 80 kDa-Protein mit zinkbindenden Eigenschaften bleibt unidentifiziert. Die Zinkbindungskapazität der fraktionierten Proteine ist dabei im Caput epididymidis am stärksten ausgeprägt. Atomabsorptionsspektralphotometrische Untersuchungen zeigen die höchsten flagellären Zinkwerte in den Spermien des Rete testis und eine Abnahme des Zinkgehalts zwischen Nebenhodenkopf und -körper. Durch Autometallographie kann eine epitheliale Zinkresorption im Nebenhodenschwanz nachgewiesen werden. Dort erfolgt auch die basale Anreicherung des Zinks. Am Zinkstoffwechsel scheint auch der Macrophage Migration Inhibitory Factor (MIF) beteiligt zu sein. Dieser ist ein Zytokin mit Oxidoreduktasecharakter und kommt unter anderem im Nebenhodenepithel sowie in den Vesikeln des Nebenhoden-Fluids der Ratte vor. MIF zeigt in den hier durchgeführten Untersuchungen sowohl in systemhomologer, als auch in rekombinanter Form in vitro eine Zink-eliminierende Wirkung auf Rattenspermatozoen des Caputs und der Cauda epididymidis und hat somit möglicherweise Einfluss auf den Reifungsprozess der Spermien im Nebenhoden. Lit.: Henkel R, Bittner J, Weber R, Hüther F, Miska W (1999). Relevance of zinc in human sperm flagella and its relation to motility. Fertil Steril 71: 1138-1143

Efecto de la hipoxia-reoxigenación y las radiaciones ionizantes en la captación de glucosa en líneas tumorales de seno y colon cocultivadas con células endoteliales.

La captación de glucosa y su conversión en lactato juega un papel fundamental en el metabolismo tumoral, independientemente de la concentración de oxígeno presente en el tejido (efecto Warburg). Sin embrago, dicha captación varía de un tipo tumoral a otro, y dentro del mismo tumor, situación que podría depender de las características microambientales tumorales (fluctuaciones de oxígeno, presencia de otros tipos celulares) y de factores estresores asociados a los tratamientos. Se estudió el efecto de la hipoxia-reoxigenación (HR) y las radiaciones ionizantes (RI) sobre la captación de glucosa, en cultivos de líneas tumorales MCF-7 y HT-29, cultivadas de forma aislada o en cocultivo con la línea celular EAhy296. Se encontró que la captación de glucosa en HR es diferente para lo descrito en condiciones de hipoxia permanente y que es modificada en el cocultivo. Se identificaron poblaciones celulares dentro de la misma línea celular, de alta y baja captación de glucosa, lo que implicaría una simbiosis metabólica de la célula como respuesta adaptativa a las condiciones tumorales. Se evaluó la expresión de NRF2 y la translocación nuclear de NRF2 y HIF1a, como vías de respuesta a estrés celular e hipoxia. La translocación nuclear de las proteínas evaluadas explicaría el comportamiento metabólico de las células tumorales de seno, pero no de colon, por lo cual deben existir otras vías metabólicas implicadas. Las diferencias en el comportamiento de las células tumorales en HR en relación con hipoxia permitirá realizar planeaciones dosimétricas más dinámicas, que reevalúen las condiciones de oxigenación tumoral constantemente.

Caracterización clínica, citoquímica y microbiológica de pacientes cirróticos con peritonitis bacteriana en la Fundación Cardioinfantil

Introducción: La peritonitis bacteriana espontanea es la infección más frecuente en pacientes cirróticos causado generalmente por Escherichia coli. Existen factores de riesgo relacionados con la aparición y recurrencia de infección peritoneal por lo que la implementación de estrategias tempranas y preventivas podría impactar en la disminución de la morbimortalidad. Metodología: Estudio descriptivo, serie de casos, se efectuó la búsqueda de los resultados del estudio citoquímico de líquidos ascíticos de pacientes entre los años 2009 y 2013, seleccionando aquellos compatibles con infección y que correspondieran a sujetos cirróticos, para posteriormente realizar la recolección de datos clínicos y paraclínicos con el fin de conformar la base de datos y finalizar con su respectivo análisis. Resultados: El alcohol es la principal causa de cirrosis en pacientes infectados; el principal microorganismo aislado fue Escherichia coli, documentando un 78% de cultivos negativos, 20% más que lo reportado por la literatura. La ampicilina sulbactam fue el antibiótico de elección en el 65% de los casos, de estos el 61% continuaron sin requerir cambio del mismo. Discusión: El presente estudio confirma al alcohol como principal etiología de cirrosis en nuestro país y a la Escherichia coli multisensible como principal agente. Debido al bajo porcentaje de cambios que requirió la ampicilina sulbactam durante el ajuste de la terapia se puede sugerir a este antibiotico dentro del manejo, sin embargo se require de estudios complementarios para comparar su efectividad en relación con cefalosporinas de tercera generación. De igual forma debe priorizarse la toma de cultivos en botellas de hemocultivos para aumentar la cantidad de aislamientos y optimizar el tratamiento antibiótico guiado de acuerdo al microorganismo obtenido.

Uso de la matriz extracelular como material para ingeniería de tejidos

Introducción: La evaluación de injertos vasculares de submucosa de intestino delgado para la regeneración de vasos sanguíneos ha producido una permeabilidad variable (0-100%) que ha sido concurrente con la variabilidad en las técnicas de fabricación. Metodología: Investigamos los efectos de fabricación en permeabilidad y regeneración en un diseño experimental de 22factorial que combino: 1) preservación (P) o remoción (R) de la capa estratum compactum del intestino, y 2) deshidratada (D) o hidratada (H), dentro de cuatro grupos de estudio (PD, RD, PH, RH). Los injertos fueron implantados en las Arterias Carótidas de porcinos (ID 4.5mm, N=4, 7d). Permeabilidad, trombogenicidad, reacción inflamatoria, vascularización, infiltración de fibroblastos, perfil de polarización de macrófagos y fuerza tensil biaxial fueron evaluadas. Resultados: Todos los injertos PD permanecieron permeables (4/4), pero tuvieron escasa vascularización e infiltración de fibroblastos. El grupo RD permaneció permeable (4/4), presentó una extensa vascularización e infiltración de fibroblastos, y el mayor número del fenotipo de macrófagos (M2) asociado a regeneración. El grupo RH presentó menor permeabilidad (3/4), una extensa vascularización e infiltración de fibroblastos, y un perfil dominante de M2. El grupo PH presentó el menor grado de permeabilidad, y a pesar de mayor infiltración celular que PD, exhibió un fenotipo de macrófagos dominante adverso. La elasticidad de los injertos R evolucionó de una manera similar a las Carótidas nativas (particularmente RD, mientras que los injertos P mantuvieron su rigidez inicial. Discusión: Concluimos que los parámetros de fabricación afectan drásticamente los resultados, siendo los injertos RD los que arrojaron mejores resultados.

Anàlisi microscòpica de l'esperma ejaculada i de la maduració epididimària dels espermatozoides de Sus domesticus

El present treball analitza la morfologia espermàtica de l'ejaculat de Sus domesticus, la histologia del conducte epididimari i la qualitat de l'esperma epididimari. El material d'estudi prové de mascles reproductors porcins de les races Landrace i Pietrain, sans i sexualment madurs. La metodologia emprada es basa en l'examen al microscopi òptic (camp dar, contrast de fases i contrast interferencial) i al microscopi electrònic (de rastreig i de transmissió). Per a l'anàlisi estadística de les dades s'ha utilitzat el test de la X2 de Pearson (p<0,01). L'estudi de la morfologia espermàtica de l'ejaculat permet distingir diversos tipus de gàmetes que s'han classificat en tres grups: espermatozoides madurs, espermatozoides immadurs i espermatozoides aberrants, així com algunes cèI.lules somàtiques. L'espermatozoide madur de Sus domesticus és un gàmeta típic de mamífer (format per tres parts: cap, peça de connexió i cua) en que destaquen: la forma oval i plana del cap, el desenvolupament d'una protuberància acrosòmica apical en una de les cares del cap i la presencia dels cossos laminars en la peça de connexió. L'espermatozoide immadur es caracteritza per la presencia de la gota citoplasmàtica, el major desenvolupament de la protuberància acrosòmica apical i per la flexibilitat del cap. Els espermatozoides aberrants es descriuen i classifiquen segons la morfologia externa i la morfologia interna, distingint-se una amplia gama de malformacions que afecten les diverses parts de l'espermatozoide. Les cèl·lules somàtiques presents en l'ejaculat ofereixen les característiques pròpies d'un macròfag i se les ha observat englobant espermatozoides immadurs. L'estudi de l'estructura i la ultraestructura de les tres regions anatòmiques de l'epidídim (caput, corpus i cauda) revela que: a) l'epiteli epididimari és pseudoestratificat amb esterocilis, b) cada regió epididimària presenta uns valors característics en relació al diàmetre intern del conducte, a l'alçada de l'epiteli, a la longitud dels esterocilis i al nombre de cèl·lules somàtiques luminals, i c) l'epiteli epididimari esta format per cinc tipus cel·lulars: les cèl·lules principals, les cèl·lules basals, les cèl·lules dares, les cèl·lules estretes i les cèl·lules basòfiles. Dels resultats obtinguts es pot deduir que: a) aquests cinc tipus cel·lulars es distribueixen al llarg del conducte epididimari de forma no homogènia, b) les cèl·lules basals, les cèl·lules principals, les cèI.Iules dares i les cèl·lules estretes són diversos estadis del desenvolupament d'un mateix tipus cel·lular especialitzat en la secreció i reabsorció cel·lular, i c) les cèl·lules basòfiles són les precursores de les cèl·lules somàtiques luminals. La qualitat de l'esperma procedent de les tres regions de l'epidídim ha estat analitzada a partir dels següents paràmetres espermàtics: vitalitat, resistència osmòtica dels acrosomes, estabilitat cefàlica, morfologia, malformacions i aglutinació. La vitalitat espermàtica disminueix progressivament al llarg del conducte epididimari. La resistència osmòtica dels acrosomes s'assoleix en la regió corporal de l'epidídim. L'estabilitat cefàlica dels espermatozoides és més elevada en les dues primeres regions de l'epidídim que en la regió caudal. Cada regió de l'epidídim es caracteritza per una morfologia espermàtica específica: a) el caput es caracteritza per l'elevat percentatge d'espermatozoides immadurs amb gota citoplasmàtica proximal, b) el corpus es caracteritza per l'elevat percentatge d'espermatozoides immadurs amb gota citoplasmàtica distal, i c) el cauda es caracteritza per l'elevat percentatge d'espermatozoides madurs. S'han estudiat les següents malformacions d'origen epididimari: espermatozoides de cua doblegada per l'anell de Jensen (origen en el cauda), espermatozoides de cua enrotllada i espermatozoides de cues fusionades (origen en el corpus). Els espermatozoides perden la capacitat de doblegar la cua per la peça intermèdia a mesura que avancen pel conducte epididimari. L'aglutinació espermàtica tendeix a augmentar progressivament al llarg del conducte epididimari, si bé, no s'han observat variacions significatives en els diversos tipus d'aglutinació. La maduració epididimaria dels espermatozoides de Sus domesticus és un procés lent i complex, i la qualitat de l'ejaculat depèn de que aquesta maduració hagi estat completa. La presencia en l'esperma ejaculat de formes gamètiques pròpies de l'esperma epididimari és un signe d'una incompleta maduració dels espermatozoides; i, pot considerar-se com un paràmetre indicador d'estrés del mascle reproductor, tant més quant més s'assembli a la morfologia espermàtica de la regió cefàlica de l'epidídim.

Immunohistochemistry of synergistic effects of kanamycin and furosemide in the murine model

Adult CBA/CaJ mice were injected with large single dose of both kanamycin and furosemide in order to study hair cell lesion and macrophage recruitment within the cochlea.

Transcriptional profiling of the LPS induced NF-kappaB response in macrophages

BACKGROUND: Exposure of macrophages to bacterial products such as lipopolysaccharide (LPS) results in activation of the NF-kappaB transcription factor, which orchestrates a gene expression programme that underpins the macrophage-dependent immune response. These changes include the induction or repression of a wide range of genes that regulate inflammation, cell proliferation, migration and cell survival. This process is tightly regulated and loss of control is associated with conditions such as septic shock, inflammatory diseases and cancer. To study this response, it is important to have in vitro model systems that reflect the behaviour of cells in vivo. In addition, it is necessary to understand the natural differences that can occur between individuals. In this report, we have investigated and compared the LPS response in macrophage derived cell lines and peripheral blood mononuclear cell (PBMC) derived macrophages. RESULTS: Gene expression profiles were determined following LPS treatment of THP-1 cells for 1 and 4 hours. LPS significantly induced or repressed 72 out of 465 genes selected as being known or putative NF-kappaB target genes, which exhibited 4 temporal patterns of expression. Results for 34 of these genes, including several genes not previously identified as LPS target genes, were validated using real time PCR. A high correlation between microarray and real time PCR data was found. Significantly, the LPS induced expression profile of THP-1 cells, as determined using real time PCR, was found to be very similar to that of human PBMC derived macrophages. Interestingly, some differences were observed in the LPS response between the two donor PBMC macrophage populations. Surprisingly, we found that the LPS response in U937 cells was dramatically different to both THP-1 and PBMC derived macrophages. CONCLUSION: This study revealed a dynamic and diverse transcriptional response to LPS in macrophages, involving both the induction and repression of gene expression in a time dependent manner. Moreover, we demonstrated that the LPS induced transcriptional response in the THP-1 cell line is very similar to primary PBMC derived macrophages. Therefore, THP-1 cells represent a good model system for studying the mechanisms of LPS and NF-kappaB dependent gene expression.

Effect of genistein and daidzein on platelet aggregation and monocyte and endothelial function

There has been much recent interest in the cardiovascular benefits of dietary isoflavones. The aim of the present in vitro studies was to investigate potential anti-thrombogenic and anti-atherogenic effects of the isoflavones genistein and daidzein in platelets, macrophages and endothelial cells. Pre-treatment with either isoflavone inhibited collagen-induced platelet aggregation in a dose-dependent manner. In a macrophage cell line (RAW 264-7) activated with interferon gamma plus lipopolysaccharide, both isoflavones were found to inhibit NO production and tumour necrosis factor alpha (TNF-alpha) secretion dose-dependently, but they did not affect mRNA levels for inducible nitric oxide synthase and cyclo-oxygenase-2. Both isoflavones also dose-dependently decreased monocyte chemoattractant protein-1 secretion induced by TNF-alpha in human umbilical vein endothelial cells. Compared with daidzein, genistein exerted greater inhibitory effects for all parameters studied. The present data contributes to our knowledge on the molecular mechanisms by which isoflavones may protect against coronary artery disease. Further studies are required to determine whether the effects of isoflavones observed in the current in vitro studies are relevant to the aetiology of coronary artery disease in vivo.

Effect of genistein and daidzein on platelet aggregation and monocyte and endothelial function

There has been much recent interest in the cardiovascular benefits of dietary isoflavones. The aim of the present in vitro studies was to investigate potential anti-thrombogenic and anti-atherogenic effects of the isoflavones genistein and daidzein in platelets, macrophages and endothelial cells. Pre-treatment with either isoflavone inhibited collagen-induced platelet aggregation in a dose-dependent manner. In a macrophage cell line (RAW 264-7) activated with interferon gamma plus lipopolysaccharide, both isoflavones were found to inhibit NO production and tumour necrosis factor alpha (TNF-alpha) secretion dose-dependently, but they did not affect mRNA levels for inducible nitric oxide synthase and cyclo-oxygenase-2. Both isoflavones also dose-dependently decreased monocyte chemoattractant protein-1 secretion induced by TNF-alpha in human umbilical vein endothelial cells. Compared with daidzein, genistein exerted greater inhibitory effects for all parameters studied. The present data contributes to our knowledge on the molecular mechanisms by which isoflavones may protect against coronary artery disease. Further studies are required to determine whether the effects of isoflavones observed in the current in vitro studies are relevant to the aetiology of coronary artery disease in vivo.

Techniques for quantifying effects of dietary antioxidants on transcription factor translocation and nitric oxide production in cultured cells

Dietary antioxidants can affect cellular processes relevant to chronic inflammatory diseases such as atherosclerosis. We have used non- standard techniques to quantify effects of the antioxidant soy isoflavones genistein and daidzein on translocation of Nuclear Factor-KB (NF-KB) and nitric oxide (NO) production, which are important in these diseases. Translocation was quantified using confocal immunofluoresecence microscopy and ratiometric image analysis. NO was quantified by an electrochemical method after reduction of its oxidation products in cell culture supernatants. Activation of the RAW 264.7 murine monocyte/macrophage cell line increased the ratio of nuclear to cytoplasmic immunostaining for NF-kB. The increase was exacerbated by pre-treatment with genistein or daidzein. To show that decreases could also be detected, pre-treatment with the pine bark extract Pycnogenol (R) r was examined, and found to reduce translocation. NO production was also increased by activation, but was reduced by pre-treatment with genistein or daidzein. In the EA. hy926 human endothelial cell line, constitutive production was detectable and was increased by thrombin. The confocal and electrochemical methods gave data that agreed with results obtained using the established electromobility shift and Griess assays, but were more sensitive, more convenient, gave more detailed information and avoided the use of radioisotopes.

Antitumour activity of [1,2-di(cyclopentadienyl)-1,2-di(p-N,N-dimethylaminophenyl)-ethanediyl] titanium dichloride in xenografted Ehrlich's ascites tumour

The effects of a new titanocene compound with an ansa ligand in the cyclopentadienyl rings, the 1,2-di(cyclopentadienyl)-1,2-di(p-NNdimethylaminophenyl)-ethanediyl] titanium dichloride (TITANOCENE X), on the growth and differentiation of granulocyte-macrophage progenitor cells [colony-forming unit-granulocyte-macrophage (CFU-GM)] and Natural killer (NK) cell activity in Ehrlich's ascites tumour (EAT)-bearing mice were studied. Myelosuppression concomitant with increased numbers of spleen CFU-GM was observed in tumour-bearing mice. Treatment of these animals with TITANOCENE X (2.5-50mg/kg/day) produced an increase in myelopoicsis, in a dose-dependent manner, and reduced spleen colony formation. In addition, the treatment of EAT-bearing mice with 3 doses of 20 or 50 mg/kg TITANOCENE X restored to normal values the reduced Natural killer cell function observed during tumour growth. In parallel, TITANOCENE X prolonged, in a dose-dependent manner, the survival of mice inoculated with Ehrlich's ascites tumour. The highest dose of 50 mg/kg prolonged in 50% the survival time of EAT-bearing mice, compared to non-treated tumour-bearing controls. In comparison with previous results from our laboratory addressing the effects of titanocenes on haematopoiesis, we observed with TITANOCENE X a similar effective profile as for bis(cyclopentadienyl) dithiocyanate titanium(IV), being both less effective than di(cyclopentadienyl) dichloro titanium(IV), since the latter not only prolonged, but also increased the rate of survival. These differences in efficacy may be due to the nature of the ansa-cyclopentadienyl ligand used in TITANOCENE X, since the C, bridge between the two cyclopentadienyl groups will increase the hydrolytic stability by an organometallic chelate effect. Also, the introduction of two dimethylamino substituents increases the water solubility of TITANOCENE X when compared to titanocene dichloride itself (c) 2006 Elsevier B.V. All rights reserved.

Analysis of second messenger pathways stimulated by different chemokines acting at the chemokine receptor

The chemokine receptor, CCR5, responds to several chemokines leading to changes in activity in several signalling pathways. Here, we investigated the ability of different chemokines to provide differential activation of pathways. The effects of five CC chemokines acting at CCR5 were investigated for their ability to inhibit forskolin- stimulated 3'-5'-cyclic adenosine monophosphate (cAMP) accumulation and to stimulate Ca2+ mobilisation. in Chinese hamster ovary (CHO) cells expressing CCR5. Macrophage inflammatory protein 1 alpha (D26A) (MIP-1 alpha (D26A), CCL3 (D26A)), regulated on activation, normal T-cell expressed and secreted (RANTES, CCLS), MIP-1 beta (CCL4) and monocyte chemoattractant protein 2 (MCP-2, CCL8) were able to inhibit forskolin -stimulated CAMP accumulation, whilst MCP-4 (CCL13) could not elicit a response. CCL3 (D26A), CCL4, CCLS, CCL8 and CCL13 were able to stimulate Ca2+ mobilisation. through CCRS, although CCL3 (D26A) and CCL5 exhibited biphasic concentration-response curves. The Ca2+ responses induced by CCL4, CCL5, CCL8 and CCL13 were abolished by pertussis toxin, whereas the response to CCL3 (D26A) was only partially inhibited by pertussis toxin, indicating G(i/o)-independent signalling induced by this chemokine. Although the rank order of potency of chemokines was similar between the two assays, certain chemokines displayed different pharmacological profiles in cAMP inhibition and Ca2+ mobilisation assays. For instance, whilst CCL13 could not inhibit forskolin-stimulated cAMP accumulation, this chemokine was able to induce Ca2+ mobilisation via CCR5. It is concluded that different chemokines acting at CCR5 can induce different pharmacological responses, which may account for the broad spectrum of chemokines that can act at CCRS. (C) 2007 Elsevier Inc. All rights reserved.

Comparative effects of six probiotic strains on immune function in vitro

There is considerable interest in the strain specificity of immune modulation by probiotics. The present study compared the immunomodulatory properties of six probiotic strains of different species and two genera in a human peripheral blood mononuclear cell (PBMC) model in vitro. Live cells of lactobacilli (Lactobacillus casei Shirota, L. rhamnosus GG, L. plantarum NCIMB 8826 and L. reuteri NCIMB 11951) and bifidobacteria (Bifidobacterium longum SP 07/3 and B. bifidum MF 20/5) were individually incubated with PBMC from seven healthy subjects for 24 h. Probiotic strains increased the proportion of CD69+ on lymphocytes, T cells, T cell subsets and natural killer (NK) cells, and increased the proportion of CD25+, mainly on lymphocytes and NK cells. The effects on activation marker expression did not appear to be strain specific. NK cell activity was significantly increased by all six strains, without any significant difference between strains. Probiotic strains increased production of IL-1β, IL-6, IL-10, TNF-α, granulocyte-macrophage colony-stimulating factor and macrophage inflammatory protein 1α to different extents, but had no effect on the production of IL-2, IL-4, IL-5 or TNF-β. The cytokines that showed strain-specific modulation included IL-10, interferon-γ, TNF-α, IL-12p70, IL-6 and monocyte chemotactic protein-1. The Lactobacillus strains tended to promote T helper 1 cytokines, whereas bifidobacterial strains tended to produce a more anti-inflammatory profile. The results suggest that there was limited evidence of strain-specific effects of probiotics with respect to T cell and NK cell activation or NK cell activity, whereas production of some cytokines was differentially influenced by probiotic strains.

Error, reproducibility and sensitivity: a pipeline for data processing of Agilent oligonucleotide expression arrays

Background: Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, to design experiments and analyse the output. Furthermore, many of the more sophisticated mathematical approaches to data analysis in the literature remain inaccessible to much of the biological research community. In this study we examine ways of extracting and analysing a large data set obtained using the Agilent long oligonucleotide transcriptomics platform, applied to a set of human macrophage and dendritic cell samples. Results: We describe and validate a series of data extraction, transformation and normalisation steps which are implemented via a new R function. Analysis of replicate normalised reference data demonstrate that intrarray variability is small (only around 2 of the mean log signal), while interarray variability from replicate array measurements has a standard deviation (SD) of around 0.5 log(2) units (6 of mean). The common practise of working with ratios of Cy5/Cy3 signal offers little further improvement in terms of reducing error. Comparison to expression data obtained using Arabidopsis samples demonstrates that the large number of genes in each sample showing a low level of transcription reflect the real complexity of the cellular transcriptome. Multidimensional scaling is used to show that the processed data identifies an underlying structure which reflect some of the key biological variables which define the data set. This structure is robust, allowing reliable comparison of samples collected over a number of years and collected by a variety of operators. Conclusions: This study outlines a robust and easily implemented pipeline for extracting, transforming normalising and visualising transcriptomic array data from Agilent expression platform. The analysis is used to obtain quantitative estimates of the SD arising from experimental (non biological) intra- and interarray variability, and for a lower threshold for determining whether an individual gene is expressed. The study provides a reliable basis for further more extensive studies of the systems biology of eukaryotic cells.