Intraoperative fluorescence delineation of head and neck cancer with a fluorescent anti-epidermal growth factor receptor nanobody.

Intraoperative near-infrared (NIR) fluorescence imaging is a technology with high potential to provide the surgeon with real-time visualization of tumors during surgery. Our study explores the feasibility for clinical translation of an epidermal growth factor receptor (EGFR)-targeting nanobody for intraoperative imaging and resection of orthotopic tongue tumors and cervical lymph node metastases. The anti-EGFR nanobody 7D12 and the negative control nanobody R2 were conjugated to the NIR fluorophore IRDye800CW (7D12-800CW and R2-800CW). Orthotopic tongue tumors were induced in nude mice using the OSC-19-luc2-cGFP cell line. Tumor-bearing mice were injected with 25 µg 7D12-800CW, R2-800CW or 11 µg 800CW. Subsequently, other mice were injected with 50 or 75 µg of 7D12-800CW. The FLARE imaging system and the IVIS spectrum were used to identify, delineate and resect the primary tumor and cervical lymph node metastases. All tumors could be clearly identified using 7D12-800CW. A significantly higher tumor-to-background ratio (TBR) was observed in mice injected with 7D12-800CW compared to mice injected with R2-800CW and 800CW. The highest average TBR (2.00 ± 0.34 and 2.72 ± 0.17 for FLARE and IVIS spectrum, respectively) was observed 24 hr after administration of the EGFR-specific nanobody. After injection of 75 µg 7D12-800CW cervical lymph node metastases could be clearly detected. Orthotopic tongue tumors and cervical lymph node metastases in a mouse model were clearly identified intraoperatively using a recently developed fluorescent EGFR-targeting nanobody. Translation of this approach to the clinic would potentially improve the rate of radical surgical resections.

Knockdown of the glucocorticoid receptor alters functional integration of newborn neurons in the adult hippocampus and impairs fear-motivated behavior.

Glucocorticoids (GCs) secreted after stress reduce adult hippocampal neurogenesis, a process that has been implicated in cognitive aspects of psychopathology, amongst others. Yet, the exact role of the GC receptor (GR), a key mediator of GC action, in regulating adult neurogenesis is largely unknown. Here, we show that GR knockdown, selectively in newborn cells of the hippocampal neurogenic niche, accelerates their neuronal differentiation and migration. Strikingly, GR knockdown induced ectopic positioning of a subset of the new granule cells, altered their dendritic complexity and increased their number of mature dendritic spines and mossy fiber boutons. Consistent with the increase in synaptic contacts, cells with GR knockdown exhibit increased basal excitability parallel to impaired contextual freezing during fear conditioning. Together, our data demonstrate a key role for the GR in newborn hippocampal cells in mediating their synaptic connectivity and structural as well as functional integration into mature hippocampal circuits involved in fear memory consolidation.

Optimization of sentinel lymph node mapping in bladder cancer using near-infrared fluorescence imaging.

BACKGROUND AND OBJECTIVES: Unlike other cancers, the Sentinel Lymph Node (SLN) procedure in bladder cancer requires special attention to the injection technique. The aim of this study was to assess feasibility and to optimize tracer injection technique for SLN mapping in bladder cancer patients using NIR fluorescence imaging. METHODS: Twenty patients with invasive bladder cancer scheduled for radical cystectomy were prospectively enrolled. Indocyanine green (ICG) bound to human serum albumin (complex ICG:HSA; 500 µM) was injected peritumourally to permit SLN mapping. ICG:HSA was first administrated serosally (n = 5), and subsequently mucosally by cystoscopic injection (n = 15). In the last cohort of 12 patients treated with cystoscopic injection, the bladder was kept filled with saline for at least 15 min. RESULTS: Fluorescent lymph nodes were observed only in the patient group with cystoscopic injection of ICG:HSA. Filling of the bladder post-injection was of added value to promote drainage of ICG:HSA to the lymph nodes, and in 11 of these 12 patients (92%) one or more NIR fluorescent lymph nodes were identified. CONCLUSIONS: The current study demonstrates proof-of-principle of using NIR fluorescence imaging for SLN identification in bladder cancer. Cystoscopic injection with distension of the bladder appears optimal for SLN mapping.

Clinical trial of combined radio- and fluorescence-guided sentinel lymph node biopsy in breast cancer.

BACKGROUND: Combining radioactive colloids and a near-infrared (NIR) fluorophore permits preoperative planning and intraoperative localization of deeply located sentinel lymph nodes (SLNs) with direct optical guidance by a single lymphatic tracer. The aim of this clinical trial was to evaluate and optimize a hybrid NIR fluorescence and radioactive tracer for SLN detection in patients with breast cancer. METHODS: Patients with breast cancer undergoing SLN biopsy were enrolled. The day before surgery, a periareolar injection of indocyanine green (ICG)-99mTc-radiolabelled nanocolloid was administered and a lymphoscintigram acquired. Blue dye was injected immediately before surgery. Intraoperative SLN localization was performed using a γ probe and the Mini-FLARE™ NIR fluorescence imaging system. Patients were divided into two dose groups, with one group receiving twice the particle density of ICG and nanocolloid, but the same dose of radioactive 99mTc. RESULTS: Thirty-two patients were enrolled in the trial. At least one SLN was identified before and during operation. All 48 axillary SLNs could be detected by γ tracing and NIR fluorescence imaging, but only 42 of them stained blue. NIR fluorescence imaging permitted detection of lymphatic vessels draining to the SLN up to 29 h after injection. Doubling the particle density did not yield a difference in fluorescence intensity (median 255 (range 98-542) versus 284 (90-921) arbitrary units; P = 0.590) or signal-to-background ratio (median 5·4 (range 3·0-15·4) versus 4·9 (3·5-16·3); P = 1·000) of the SLN. CONCLUSION: The hybrid NIR fluorescence and radioactive tracer permitted accurate preoperative and intraoperative detection of the SLNs in patients with breast cancer. REGISTRATION NUMBER: NTR3685 (Netherlands Trial Register; http://www.trialregister.nl).

Dose optimization for near-infrared fluorescence sentinel lymph node mapping in patients with melanoma.

BACKGROUND: Regional lymph node involvement is the most important prognostic factor in cutaneous melanoma. As only 20% of patients with melanoma have occult nodal disease and would benefit from a regional lymphadenectomy, the sentinel lymph node (SLN) biopsy was introduced. Near-infrared (NIR) fluorescence has been hypothesized to improve SLN mapping. OBJECTIVES: To assess the potential of intraoperative NIR fluorescence imaging to improve SLN mapping in patients with melanoma and to examine the optimal dose of indocyanine green adsorbed to human serum albumin (ICG:HSA). METHODS: Fifteen consecutive patients with cutaneous melanoma underwent the standard SLN procedure using (99m) technetium-nancolloid and patent blue. In addition, intraoperative NIR fluorescence imaging was performed after injection of 1·6 mL of 600, 800, 1000 or 1200 µmolL(-1) of ICG: HSA in four quadrants around the primary excision scar. RESULTS: NIR fluorescence SLN mapping was successful in 93% of patients. In one patient, no SLN could be identified using either conventional methods or NIR fluorescence. A total of 30 SLNs (average 2·0, range 1-7) were detected, 30 radioactive (100%), 27 blue (73%) and 30 NIR fluorescent (100%). With regard to the effect of concentration on signal-to-background ratios a trend (P=0·066) was found favouring the 600, 800 and 1000 µmol L(-1) groups over the 1200 µmol L(-1) group. CONCLUSION: This study demonstrates feasibility and accuracy of SLN mapping using ICG: HSA. Considering safety, cost and pharmacological characteristics, an ICG: HSA concentration of 600 µmolL(-1) appears optimal for SLN mapping in cutaneous melanoma, although lower doses need to be assessed.

Near-infrared fluorescence sentinel lymph node biopsy in vulvar cancer: a randomised comparison of lymphatic tracers.

This study aims to confirm the feasibility of near-infrared (NIR) fluorescence imaging for sentinel lymph node (SLN) biopsy in vulvar cancer and to compare the tracer indocyanine green (ICG) bound to human serum albumin (HSA) versus ICG alone. Women received 99mTc-nanocolloid and patent blue for SLN detection. Subsequently, women randomly received ICG:HSA or ICG alone. In 24 women, 35 SLNs were intraoperatively detected. All SLNs detected were radioactive and NIR fluorescent and 27 (77%) were blue. No significant difference was found between ICG:HSA and ICG alone. This trial confirms the feasibility of NIR fluorescence imaging for SLN mapping in vulvar cancer.

Automated detection of irradiated food with the comet assay.

Food irradiation is the process of exposing food to ionising radiation in order to disinfect, sanitise, sterilise and preserve food or to provide insect disinfestation. Irradiated food should be adequately labelled according to international and national guidelines. In many countries, there are furthermore restrictions to the product-specific maximal dose that can be administered. Therefore, there is a need for methods that allow detection of irradiated food, as well as for methods that provide a reliable dose estimate. In recent years, the comet assay was proposed as a simple, rapid and inexpensive method to fulfil these goals, but further research is required to explore the full potential of this method. In this paper we describe the use of an automated image analysing system to measure DNA comets which allow the discrimination between irradiated and non-irradiated food as well as the set-up of standard dose-response curves, and hence a sufficiently accurate dose estimation.

Antitumor activity, induction of cross-resistance, and nephrotoxicity of a new platinum analogue, cis-1,1-diaminomethylcyclohexaneplatinum(II) sulfate, and of cis-diamminedichloroplatinum(II) in an immunocytoma model in the LOU/M rat.

A newly synthesized platinum analogue, cis-1,1-diaminomethylcyclohexaneplatinum(II) sulfate (TNO-6), was compared with cis-diamminedichloroplatinum(II) (cis-DDP) for antitumor activity and nephrotoxicity. Antitumor activity was determined in an IgM immunocytoma model in the LOU/M rat. Tumor cells were inoculated on the left flank, and therapy was started when a tumor diameter of 10 to 30 mm was reached. At the start of the therapy, the primary tumor had already metastasized to the draining lymph node and liver. Both platinum compounds, dissolved in 5% glucose water, induced an almost complete tumor regression within 10 to 14 days (average, 84% tumor load reduction) and prolonged survival, compared to that of nontreated animals. The antitumor activity induced by repeated i.p. administration of cis-DDP and TNO-6 reached its maximum at a dose of 1.0 mg/kg body weight (twice a week for 7 weeks). This treatment regimen resulted in a highest tolerable dose for cis-DDP of 1.0 mg/kg and for TNO-6 of 2.0 mg/kg. However, when rats were treated with a 2.0-mg/kg dose of TNO-6, no increase in antitumor activity was obtained. For both platinum compounds, tumor recurrence occurred in almost all animals within 2 to 7 days after the maximum tumor load reduction. Tumors that recurred were found to be cross-resistant to both platinum compounds tested but were sensitive to treatment with doxorubicin (Adriamycin). With regard to toxicity, repeated administration of TNO-6 (1.0 mg/kg twice a week for 7 weeks) induced less decrease of body weight than did cis-DDP. For TNO-6, even in the highest dose investigated (2.0 mg/kg twice a week for 7 weeks), no nephrotoxicity was observed on histological examination of kidney and blood urea and creatinine values, whereas for cis-DDP nephrotoxicity was still present in the lowest dose investigated (0.5 mg/kg). From the comparison of the antitumor activity and nephrotoxicity of TNO-6 and cis-DDP, administered i.p. in 5% glucose solution, it is concluded that both drugs have comparable antitumor activity and potency. In contrast to the effects of cis-DDP, no nephrotoxicity was observed with TNO-6; thus, TNO-6 might be a good alternative to cis-DDP in avoiding nephrotoxicity during platinum therapy.

Developmental bioinformatics: linking genetic data to virtual embryos.

This paper discusses current efforts to produce databases of gene expression for the major model embryos used in developmental biology. The efforts to build these resources were motivated by the need for immediate internet access to all types of research data, and the production of these databases is a major and new challenge for bioinformatics. Thus far bioinformatics has mainly been concerned with textually oriented resources and data, much of it concerned with gene and protein sequences. Because the genetic basis of developmental biology is integrated with developmental anatomy, these databases require the use of images to link molecular data with spatial information. In order to standardise database formats, digital atlases of some model systems are being produced that include integrated anatomical descriptions and these are being linked to appropriate genetic data. Integrating such image-based, searchable data into databases makes new demands on the field of bioinformatics and we consider here the imaging modalities that are used to obtain information and we discuss in particular the production of 3D images from serial sections. Next, we consider how to integrate textual and spatial descriptions of gene expression and the key tool needed to make this possible, i.e. anatomical nomenclature. A short review of internet resources on developmental biology is also given and future prospects for the development of these databases are discussed.

Atrioventricular conduction system in hearts with muscular ventricular septal defects in the setting of complete transposition.

The detailed structure of a ventricular septal defect was compared in 90 hearts with complete transposition (concordant atrioventricular and discordant ventriculoarterial connections) and in 102 hearts with concordant connections at both junctions; the latter group was selected to include only cases with the septums aligned in the normal way. The interventricular communications observed in 13% of the group with complete transposition, which, in our material, had no counterpart in the hearts with concordant segmental connections, were of special interest. These defects, completely surrounded by muscle, were positioned around the midline on the right side of the septum but always lay under or partially under the septal leaflet of the tricuspid valve. The medial papillary muscle group was always to the "left hand margin" of the defect as seen by the surgeon. Because these defects lay within the boundaries set by the septal leaflet of the tricuspid valve, they would conform to the criteria for classification as inlet muscular defects but could equally be described as central or subtricuspid. It is significant that, in all those cases with histologic sectioning, the axis of atrioventricular conduction tissue ran to the surgeon's right hand margin. This position is markedly different from the pattern found in typical defects of the inlet septum, which are completely surrounded by muscle and extend to the posterior wall of the heart. In this more common situation, the conduction axis runs above the left hand margin of the defect. This finding has obvious implications for surgical treatment.

Design and implementation of a database and program for 3D reconstruction from serial sections: a data-driven approach.

This paper describes a structural approach for a standard setup of a computer program for 3D reconstruction from serial sections. Three-dimensional reconstruction as a technique increases in importance as, along with modern immunohistochemical techniques, it is a tool in the understanding of three-dimensional development patterns. In order to apply 3D reconstruction technique in a standard laboratory setup, an attempt was made to streamline the input and the manipulation of the data such that results are obtained easily. One will find a combination of two approaches in this paper: the first is a strict ordering of the complex data, and the second is an ordering of the processes that one wishes to apply on the data (together, these two approaches constitute an information analysis); because it was observed that developmental biologists tend to work from simple lines to describe their observations, the contour model was chosen as the vehicle to build a reconstruction model from. Consequently, the data is ordered in a database that has to be manipulated to get the data out in the desired format. The most important output format is a display of the reconstructed contour stack on a graphical computer screen. Together with the other data manipulation processes, such as the input, the inspection, the revision (correction), and the reconstruction, all processes are described using the reconstruction of an 11 embryonic days (ED) rat embryo as an example. Finally, the merits of the program are illustrated with an example from the development of the human embryonic heart.

Measurement of co-localization of objects in dual-colour confocal images.

A method to measure the degree of co-localization of objects in confocal dual-colour images has been developed. This image analysis produced two coefficients that represent the fraction of co-localizing objects in each component of a dual-channel image. The generation of test objects with a Gaussian intensity distribution, at well-defined positions in both components of dual-channel images, allowed an accurate investigation of the reliability of the procedure. To do that, the co-localization coefficients were determined before degrading the image with background, cross-talk and Poisson noise. These synthesized sources of image deterioration represent sources of deterioration that must be dealt with in practical confocal imaging, namely dark current, non-specific binding and cross-reactivity of fluorescent probes, optical cross-talk and photon noise. The degraded images were restored by filtering and cross-talk correction. The co-localization coefficients of the restored images were not significantly different from those of the original undegraded images. Finally, we tested the procedure on images of real biological specimens. The results of these tests correspond with data found in the literature. We conclude that the co-localization coefficients can provide relevant quantitative information about the positional relation between biological objects or processes.

Voltammetric study of the redox behaviour of the Hg(II)/Hg(I)/Hg system at a rotating metal-ring/glassy-carbon disc electrode.

The reduction of Hg(II) at a glassy-carbon electrode in various electrolytes has been studied by rotating ring-disc voltammetry. Reduction proceeds directly to metallic mercury in a single 2-electron step. However, at the foot of the wave, and only during the first reduction sweep after pretreatment of the electrode surface, a small amount of Hg(I) species is detected at the ring. The appearance of an Hg(I) intermediate is most pronounced in sulphuric acid solution. The reduction of Hg(II) is found to proceed irreversibly and to be of first order. At sufficiently negative potentials the reduction is convective-diffusion controlled. Stripping voltammetric experiments indicate that the dissolution of mercury gives Hg(II) in complexing electrolytes. In non-complexing electrolytes the initially formed Hg(II) reacts with mercury atoms on the electrode surface to give Hg(I). During electrodissolution, two stripping peaks may be observed as a result of underpotential adsorption of mercury on glassy carbon. The difference in peak potential between the adsorption (mono) layer peak and the bulk mercury peak has been related to the difference in work functions of the deposit (mercury) and substrate (carbon). A rotating glassy-carbon electrode has been used for the anodic stripping determination of mercury. When an appropriate amount of a cation such as cadmium(II) or copper(II) is added to the test solution, mercury down to 2 x 10(-9)M (0.4 ng ml ) can be determined in acidified thiocyanate electrolyte with a relative standard deviation of about 22%.

Catalytic influence of Cl(-), Br(-), I(-) and SCN(-) on the cyclic voltammetric behaviour of Sb(III).

The electrocatalysis of the reduction of Sb(III) ions at a mercury electrode by Cl(-), Br(-), I(-) and SCN(-) ions and its dependence on the hydrogen-ion concentration has been studied in 4M (H, Na)ClO(4) solutions by cyclic voltammetry. The electrocatalytic capacity increases considerably in the order Cl(-) < SCN(-) < Br(-) < I(-) and a ligand-bridging mechanism is probably involved. Increasing the acidity at constant bridging-ligand concentration enhances the reaction rate. This can be explained by assuming that the influence of the hydrogen-ion concentration on the bridged activated complex is the same as on the Sb(III) complexes present in the bulk of the solution. From an analytical point of view it is important that the reduction of Sb(III) ions at a mercury electrode proceeds reversibly in the presence of Cl(-), Br(-), I(-) or SCN(-) ions.

3D base: a geometrical data base system for the analysis and visualisation of 3D-shapes obtained from parallel serial sections including three different geometrical representations.

In this paper we discuss a geometrical data base that includes three different geometrical representations of one and the same reconstructed 3D shape: the contour-pile, the voxel enumeration, and the triangulation of a surface. The data base is tailored for 3D shapes obtained from plan-parallel serial sections. It is explained how this geometrical data base is useful with the different processing approaches of a 3D shape, such as analysis and visualisation. Methods of conversion between the geometrical representations are discussed. Examples of the operation of the data base as it is embedded in a data base management system are given by illustrations of retrieval of geometrical information.

Annexin A2 depletion delays EGFR endocytic trafficking via cofilin activation and enhances EGFR signaling and metastasis formation.

Enhanced epidermal growth factor receptor (EGFR) activity has been strongly linked to breast cancer progression and mediators of EGFR endocytosis may well be involved. We developed a semi-automated high-content fluorescence microscopy-based EGFR endocytosis screen to identify proteins that mediate EGFR endocytosis in human HBL100 breast cancer cells. Knockdown of 172 individual endocytosis and actin-regulatory genes with small interfering RNAs led to the identification of 14 genes of which the contribution to EGFR endocytosis in breast cancer is until now poorly defined, including DNAJC6, GDI2, FGD6, HAX1, NECAP2 and AnxA2. We show that depletion of the actin and endocytosis regulatory protein annexin A2 (AnxA2) in a panel of four triple negative breast cancer (TNBC) cell lines affected EGFR endocytosis. Depletion of AnxA2 in the aggressive and highly metastatic MDA-MB-231 TNBC cell line resulted in the inhibition of EGFR transport beyond the early endosomes. This inhibition coincided with enhanced epidermal growth factor (EGF)-induced cell migration and downstream signaling via c-Jun N-terminal kinase (JNK) and Akt. Moreover, AnxA2 knockdown increased lung metastasis formation in mice. The effect of AnxA2 knockdown on EGFR endocytosis in MDA-MB-231 was related to dephosphorylation/activation of the actin-severing protein cofilin, as re-expression of an inactive S3E-cofilin mutant, but not an active S3A-cofilin mutant, re-established EGFR endocytosis to control levels. Together, our data provide evidence for AnxA2 as a mediator of EGFR endocytosis and signaling in breast cancer via regulation of cofilin activation.

Real-time intraoperative detection of breast cancer using near-infrared fluorescence imaging and Methylene Blue.

BACKGROUND: Despite recent developments in preoperative breast cancer imaging, intraoperative localization of tumor tissue can be challenging, resulting in tumor-positive resection margins during breast conserving surgery. Based on certain physicochemical similarities between Technetium((99m)Tc)-sestamibi (MIBI), an SPECT radiodiagnostic with a sensitivity of 83-90% to detect breast cancer preoperatively, and the near-infrared (NIR) fluorophore Methylene Blue (MB), we hypothesized that MB might detect breast cancer intraoperatively using NIR fluorescence imaging. METHODS: Twenty-four patients with breast cancer, planned for surgical resection, were included. Patients were divided in 2 administration groups, which differed with respect to the timing of MB administration. N = 12 patients per group were administered 1.0 mg/kg MB intravenously either immediately or 3 h before surgery. The mini-FLARE imaging system was used to identify the NIR fluorescent signal during surgery and on post-resected specimens transferred to the pathology department. Results were confirmed by NIR fluorescence microscopy. RESULTS: 20/24 (83%) of breast tumors (carcinoma in N = 21 and ductal carcinoma in situ in N = 3) were identified in the resected specimen using NIR fluorescence imaging. Patients with non-detectable tumors were significantly older. No significant relation to receptor status or tumor grade was seen. Overall tumor-to-background ratio (TBR) was 2.4 ± 0.8. There was no significant difference between TBR and background signal between administration groups. In 2/4 patients with positive resection margins, breast cancer tissue identified in the wound bed during surgery would have changed surgical management. Histology confirmed the concordance of fluorescence signal and tumor tissue. CONCLUSIONS: This feasibility study demonstrated an overall breast cancer identification rate using MB of 83%, with real-time intraoperative guidance having the potential to alter patient management.

The embryonic expression patterns of zebrafish genes encoding LysM-domains.

The function and structure of LysM-domain containing proteins are very diverse. Although some LysM domains are able to bind peptidoglycan or chitin type carbohydrates in bacteria, in fungi and in plants, the function(s) of vertebrate LysM domains and proteins remains largely unknown. In this study we have identified and annotated the six zebrafish genes of this family, which encode at least ten conceptual LysM-domain containing proteins. Two distinct sub-families called LysMD and OXR were identified and shown to be highly conserved across vertebrates. The detailed characterization of LysMD and OXR gene expression in zebrafish embryos showed that all the members of these sub-families are strongly expressed maternally and zygotically from the earliest stages of a vertebrate embryonic development. Moreover, the analysis of the spatio-temporal expression patterns, by whole mount and fluorescent in situ hybridizations, demonstrates pronounced LysMD and OXR gene expression in the zebrafish brain and nervous system during stages of larval development. None of the zebrafish LysMD or OXR genes was responsive to challenge with bacterial pathogens in embryo models of Salmonella and Mycobacterium infections. In addition, the expression patterns of the OXR genes were mapped in a zebrafish brain atlas.

p140Cap suppresses the invasive properties of highly metastatic MTLn3-EGFR cells via impaired cortactin phosphorylation.

We have recently shown that the adaptor protein p140Cap regulates tumor properties in terms of cell motility and growth. Here, by using the highly metastatic rat adenocarcinoma cell line MTLn3-epidermal growth factor receptor (EGFR), we assess the role of p140Cap in metastasis formation. Orthotopic transplantation of MTLn3-EGFR cells over-expressing p140Cap in Rag2(-/-)γ(c)(-/-) mice resulted in normal primary tumor growth compared with the controls. Strikingly, p140Cap over-expression causes an 80% inhibition in the number of lung metastases. p140Cap over-expressing cells display a 50% reduction in directional cell migration, an increased number and size of focal adhesions, and a strong impairment in the ability to invade in a 3D matrix. p140Cap over-expression affects EGFR signaling and tyrosine phosphorylation of cortactin in response to EGF stimulation. Intriguingly, p140Cap associates with cortactin via interaction with its second proline-rich domain to the cortactin SH3 domain. The phosphomimetic cortactin tyrosine 421 mutant rescues migration and invasive properties in p140Cap over-expressing cells. Taken together, these data demonstrate that p140Cap suppresses the invasive properties of highly metastatic breast carcinoma cells by inhibiting cortactin-dependent cell motility.

Mining and analysing spatio-temporal patterns of gene expression in an integrative database framework.

Mining patterns of gene expression provides a crucial approach in discovering knowledge such as finding genetic networks that underpin the embryonic development. Analysis of mining results and evaluation of their relevance in the domain remains a major concern. In this paper we describe our explorative studies in support of solutions to facilitate the analysis and interpretation of mining results. In our particular case we describe a solution that is found in the extension of the Gene Expression Management System (GEMS), i.e. an integrative framework for spatio-temporal organization of gene expression patterns of zebrafish to a framework supporting data mining, data analysis and patterns interpretation As a proof of principle, the GEMS has been equipped with data mining functionality suitable for spatio-temporal tracking, thereby generating added value to the submission of data for data mining and analysis. The analysis of the genetic networks is based on the availability of domain ontologies which dynamically provides meaning to the discovered patterns of gene expression data. Combination of data mining with the already presently available capabilities of GEMS will significantly augment current data processing and functional analysis strategies.