Publications by authors named "Marco Fato"

36 Publications

In vitro models replicating the human intestinal epithelium for absorption and metabolism studies: A systematic review.

J Control Release 2021 Jul 24;335:247-268. Epub 2021 May 24.

National Research Council of Italy, Institute of Electronics, Computer and Telecommunications (IEIIT) Institute, 16149 Genoa, Italy. Electronic address:

Absorption, distribution, metabolism and excretion (ADME) studies represent a fundamental step in the early stages of drug discovery. In particular, the absorption of orally administered drugs, which occurs at the intestinal level, has gained attention since poor oral bioavailability often led to failures for new drug approval. In this context, several in vitro preclinical models have been recently developed and optimized to better resemble human physiology in the lab and serve as an animal alternative to accomplish the 3Rs principles. However, numerous models are ineffective in recapitulating the key features of the human small intestine epithelium and lack of prediction potential for drug absorption and metabolism during the preclinical stage. In this review, we provide an overview of in vitro models aimed at mimicking the intestinal barrier for pharmaceutical screening. After briefly describing how the human small intestine works, we present i) conventional 2D synthetic and cell-based systems, ii) 3D models replicating the main features of the intestinal architecture, iii) micro-physiological systems (MPSs) reproducing the dynamic stimuli to which cells are exposed in the native microenvironment. In this review, we will highlight the benefits and drawbacks of the leading intestinal models used for drug absorption and metabolism studies.
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http://dx.doi.org/10.1016/j.jconrel.2021.05.028DOI Listing
July 2021

High blood flow shear stress values are associated with circulating tumor cells cluster disaggregation in a multi-channel microfluidic device.

PLoS One 2021 14;16(1):e0245536. Epub 2021 Jan 14.

National Research Council (CNR), Institute of Electronic, Computer and Telecommunications (IEIIT), Genoa, Italy.

Metastasis represents a dynamic succession of events involving tumor cells which disseminate through the organism via the bloodstream. Circulating tumor cells (CTCs) can flow the bloodstream as single cells or as multicellular aggregates (clusters), which present a different potential to metastasize. The effects of the bloodstream-related physical constraints, such as hemodynamic wall shear stress (WSS), on CTC clusters are still unclear. Therefore, we developed, upon theoretical and CFD modeling, a new multichannel microfluidic device able to simultaneously reproduce different WSS characterizing the human circulatory system, where to analyze the correlation between SS and CTC clusters behavior. Three physiological WSS levels (i.e. 2, 5, 20 dyn/cm2) were generated, reproducing values typical of capillaries, veins and arteries. As first validation, triple-negative breast cancer cells (MDA-MB-231) were injected as single CTCs showing that higher values of WSS are correlated with a decreased viability. Next, the SS-mediated disaggregation of CTC clusters was computationally investigated in a vessels-mimicking domain. Finally, CTC clusters were injected within the three different circuits and subjected to the three different WSS, revealing that increasing WSS levels are associated with a raising clusters disaggregation after 6 hours of circulation. These results suggest that our device may represent a valid in vitro tool to carry out systematic studies on the biological significance of blood flow mechanical forces and eventually to promote new strategies for anticancer therapy.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0245536PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7808575PMC
June 2021

Spontaneous movements in the newborns: a tool of quantitative video analysis of preterm babies.

Comput Methods Programs Biomed 2021 Feb 21;199:105838. Epub 2020 Nov 21.

DIBRIS dept., University of Genoa, Genoa, Italy; RBCS dept., Italian Institute of Technology, Genoa, Italy. Electronic address:

Background And Objectives: The number of preterm babies is steadily growing world-wide and these neonates are at risk of neuro-motor-cognitive deficits. The observation of spontaneous movements in the first three months of age is known to predict such risk. However, the analysis by specifically trained physiotherapists is not suited for the clinical routine, motivating the development of simple computerized video analysis systems, integrated with a well-structured Biobank to make available for preterm babies a growing service with diagnostic, prognostic and epidemiological purposes.

Methods: MIMAS (Markerless Infant Movement Analysis System) is a simple, low-cost system of video analysis of spontaneous movements of newborns in their natural environment, based on a single standard RGB camera, without markers attached to the body. The original videos are transformed into binarized sequences highlighting the silhouette of the baby, in order to minimize the illumination effects and increase the robustness of the analysis; such sequences are then coded by a large set of parameters (39) related to the spatial and spectral changes of the silhouette. The parameter vectors of each baby were stored in the Biobank together with related clinical information.

Results: The preliminary test of the system was carried out at the Gaslini Pediatric Hospital in Genoa, where 46 preterm (PT) and 21 full-term (FT) babies (as controls) were recorded at birth (T0) and 8-12 weeks thereafter (T1). A simple statistical analysis of the data showed that the coded parameters are sensitive to the degree of maturation of the newborns (comparing T0 with T1, for both PT and FT babies), and to the conditions at birth (PT vs. FT at T0), whereas this difference tends to vanish at T1. Moreover, the coding method seems also able to detect the few 'abnormal' preterm babies in the PT populations that were analyzed as specific case studies.

Conclusions: Preliminary results motivate the adoption of this tool in clinical practice allowing for a systematic accumulation of cases in the Biobank, thus for improving the accuracy of data analysis performed by MIMAS and ultimately allowing the adoption of data mining techniques.
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http://dx.doi.org/10.1016/j.cmpb.2020.105838DOI Listing
February 2021

3D Perfusable Hydrogel Recapitulating the Cancer Dynamic Environment to in Vitro Investigate Metastatic Colonization.

Polymers (Basel) 2020 Oct 24;12(11). Epub 2020 Oct 24.

National Research Council of Italy, Institute of Electronic, Computer and Telecommunications (IEIIT) Institute, 16149 Genoa, Italy.

Metastasis is a dynamic process involving the dissemination of circulating tumor cells (CTCs) through blood flow to distant tissues within the body. Nevertheless, the development of an in vitro platform that dissects the crucial steps of metastatic cascade still remains a challenge. We here developed an in vitro model of extravasation composed of (i) a single channel-based 3D cell laden hydrogel representative of the metastatic site, (ii) a circulation system recapitulating the bloodstream where CTCs can flow. Two polymers (i.e., fibrin and alginate) were tested and compared in terms of mechanical and biochemical proprieties. Computational fluid-dynamic (CFD) simulations were also performed to predict the fluid dynamics within the polymeric matrix and, consequently, the optimal culture conditions. Next, once the platform was validated through perfusion tests by fluidically connecting the hydrogels with the external circuit, highly metastatic breast cancer cells (MDA-MB-231) were injected and exposed to physiological wall shear stress (WSS) conditions (5 Dyn/cm) to assess their migration toward the hydrogel. Results indicated that CTCs arrested and colonized the polymeric matrix, showing that this platform can be an effective fluidic system to model the first steps occurring during the metastatic cascade as well as a potential tool to in vitro elucidate the contribution of hemodynamics on cancer dissemination to a secondary site.
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http://dx.doi.org/10.3390/polym12112467DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7690854PMC
October 2020

Quantitative susceptibility map analysis in preterm neonates with germinal matrix-intraventricular hemorrhage.

J Magn Reson Imaging 2018 11 10;48(5):1199-1207. Epub 2018 May 10.

Neuroradiology Unit, Istituto Giannina Gaslini, Genoa, Italy.

Background: Germinal matrix-intraventricular hemorrhage (GMH-IVH) is a common form of intracranial hemorrhage occurring in preterm neonates that may affect normal brain development. Although the primary lesion is easily identified on MRI by the presence of blood products, its exact extent may not be recognizable with conventional sequences. Quantitative susceptibility mapping (QSM) quantify the spatial distribution of magnetic susceptibility within biological tissues, including blood degradation products.

Purpose/hypothesis: To evaluate magnetic susceptibility of normal-appearing white (WM) and gray matter regions in preterm neonates with and without GMH-IVH.

Study Type: Retrospective case-control.

Population: A total of 127 preterm neonates studied at term equivalent age: 20 had mild GMH-IVH (average gestational age 28.7 ± 2.1 weeks), 15 had severe GMH-IVH (average gestational age 29.3 ± 1.8 weeks), and 92 had normal brain MRI (average gestational age 29.8 ± 1.8 weeks).

Field Strength/sequence: QSM at 1.5 Tesla.

Assessment: QSM analysis was performed for each brain hemisphere with a region of interest-based approach including five WM regions (centrum semiovale, frontal, parietal, temporal, and cerebellum), and a subcortical gray matter region (basal ganglia/thalami).

Statistical Tests: Changes in magnetic susceptibility were explored using a one-way analysis of covariance, according to GMH-IVH severity (P < 0.05).

Results: In preterm neonates with normal brain MRI, all white and subcortical gray matter regions had negative magnetic susceptibility values (diamagnetic). Neonates with severe GMH-IVH showed higher positive magnetic susceptibility values (i.e. paramagnetic) in the centrum semiovale (0.0019 versus -0.0014 ppm; P < 0.001), temporal WM (0.0011 versus -0.0012 ppm; P = 0.037), and parietal WM (0.0005 versus -0.0001 ppm; P = 0.002) compared with controls. No differences in magnetic susceptibility were observed between neonates with mild GMH-IVH and controls (P = 0.236).

Data Conclusion: Paramagnetic susceptibility changes occur in several normal-appearing WM regions of neonates with severe GMH-IVH, likely related to the accumulation of hemosiderin/ferritin iron secondary to diffusion of extracellular hemoglobin from the ventricle into the periventricular WM.

Level Of Evidence: 4 Technical Efficacy: Stage 3 J. Magn. Reson. Imaging 2018;47:1199-1207.
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http://dx.doi.org/10.1002/jmri.26163DOI Listing
November 2018

A new cell-laden 3D Alginate-Matrigel hydrogel resembles human breast cancer cell malignant morphology, spread and invasion capability observed "in vivo".

Sci Rep 2018 03 28;8(1):5333. Epub 2018 Mar 28.

National Research Council (CNR) - IEIIT Institute, Genoa, 16149, Italy.

Purpose of this study was the development of a 3D material to be used as substrate for breast cancer cell culture. We developed composite gels constituted by different concentrations of Alginate (A) and Matrigel (M) to obtain a structurally stable-in-time and biologically active substrate. Human aggressive breast cancer cells (i.e. MDA-MB-231) were cultured within the gels. Known the link between cell morphology and malignancy, cells were morphologically characterized and their invasiveness correlated through an innovative bioreactor-based invasion assay. A particular type of gel (i.e. 50% Alginate, 50% Matrigel) emerged thanks to a series of significant results: 1. cells exhibited peculiar cytoskeleton shapes and nuclear fragmentation characteristic of their malignancy; 2. cells expressed the formation of the so-called invadopodia, actin-based protrusion of the plasma membrane through which cells anchor to the extracellular matrix; 3. cells were able to migrate through the gels and attach to an engineered membrane mimicking the vascular walls hosted within bioreactor, providing a completely new 3D in vitro model of the very precursor steps of metastasis.
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http://dx.doi.org/10.1038/s41598-018-23250-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5871779PMC
March 2018

Improvement in White Matter Tract Reconstruction with Constrained Spherical Deconvolution and Track Density Mapping in Low Angular Resolution Data: A Pediatric Study and Literature Review.

Front Pediatr 2017 30;5:182. Epub 2017 Aug 30.

Department of Informatics, Bioengineering, Robotics and System Engineering (DIBRIS), University of Genoa, Genoa, Italy.

Introduction: Diffusion-weighted magnetic resonance imaging (DW-MRI) allows noninvasive investigation of brain structure . Diffusion tensor imaging (DTI) is a frequently used application of DW-MRI that assumes a single main diffusion direction per voxel, and is therefore not well suited for reconstructing crossing fiber tracts. Among the solutions developed to overcome this problem, constrained spherical deconvolution with probabilistic tractography (CSD-PT) has provided superior quality results in clinical settings on adult subjects; however, it requires particular acquisition parameters and long sequences, which may limit clinical usage in the pediatric age group. The aim of this work was to compare the results of DTI with those of track density imaging (TDI) maps and CSD-PT on data from neonates and children, acquired with low angular resolution and low b-value diffusion sequences commonly used in pediatric clinical MRI examinations.

Materials And Methods: We analyzed DW-MRI studies of 50 children (eight neonates aged 3-28 days, 20 infants aged 1-8 months, and 22 children aged 2-17 years) acquired on a 1.5 T Philips scanner using 34 gradient directions and a b-value of 1,000 s/mm. Other sequence parameters included 60 axial slices; acquisition matrix, 128 × 128; average scan time, 5:34 min; voxel size, 1.75 mm × 1.75 mm × 2 mm; one b = 0 image. For each subject, we computed principal eigenvector (EV) maps and directionally encoded color TDI maps (DEC-TDI maps) from whole-brain tractograms obtained with CSD-PT; the cerebellar-thalamic, corticopontocerebellar, and corticospinal tracts were reconstructed using both CSD-PT and DTI. Results were compared by two neuroradiologists using a 5-point qualitative score.

Results: The DEC-TDI maps obtained presented higher anatomical detail than EV maps, as assessed by visual inspection. In all subjects, white matter (WM) tracts were successfully reconstructed using both tractography methodologies. The mean qualitative scores of all tracts obtained with CSD-PT were significantly higher than those obtained with DTI (-value < 0.05 for all comparisons).

Conclusion: CSD-PT can be successfully applied to DW-MRI studies acquired at 1.5 T with acquisition parameters adapted for pediatric subjects, thus providing TDI maps with greater anatomical detail. This methodology yields satisfactory results for clinical purposes in the pediatric age group.
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http://dx.doi.org/10.3389/fped.2017.00182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5582070PMC
August 2017

A dataset of stereoscopic images and ground-truth disparity mimicking human fixations in peripersonal space.

Sci Data 2017 03 28;4:170034. Epub 2017 Mar 28.

DIBRIS-University of Genoa, Genoa, GE 16145, Italy.

Binocular stereopsis is the ability of a visual system, belonging to a live being or a machine, to interpret the different visual information deriving from two eyes/cameras for depth perception. From this perspective, the ground-truth information about three-dimensional visual space, which is hardly available, is an ideal tool both for evaluating human performance and for benchmarking machine vision algorithms. In the present work, we implemented a rendering methodology in which the camera pose mimics realistic eye pose for a fixating observer, thus including convergent eye geometry and cyclotorsion. The virtual environment we developed relies on highly accurate 3D virtual models, and its full controllability allows us to obtain the stereoscopic pairs together with the ground-truth depth and camera pose information. We thus created a stereoscopic dataset: GENUA PESTO-GENoa hUman Active fixation database: PEripersonal space STereoscopic images and grOund truth disparity. The dataset aims to provide a unified framework useful for a number of problems relevant to human and computer vision, from scene exploration and eye movement studies to 3D scene reconstruction.
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http://dx.doi.org/10.1038/sdata.2017.34DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5369322PMC
March 2017

Consistency of EEG source localization and connectivity estimates.

Neuroimage 2017 05 12;152:590-601. Epub 2017 Mar 12.

Machine Learning Department, Technische Universität Berlin, Berlin, Germany. Electronic address:

As the EEG inverse problem does not have a unique solution, the sources reconstructed from EEG and their connectivity properties depend on forward and inverse modeling parameters such as the choice of an anatomical template and electrical model, prior assumptions on the sources, and further implementational details. In order to use source connectivity analysis as a reliable research tool, there is a need for stability across a wider range of standard estimation routines. Using resting state EEG recordings of N=65 participants acquired within two studies, we present the first comprehensive assessment of the consistency of EEG source localization and functional/effective connectivity metrics across two anatomical templates (ICBM152 and Colin27), three electrical models (BEM, FEM and spherical harmonics expansions), three inverse methods (WMNE, eLORETA and LCMV), and three software implementations (Brainstorm, Fieldtrip and our own toolbox). Source localizations were found to be more stable across reconstruction pipelines than subsequent estimations of functional connectivity, while effective connectivity estimates where the least consistent. All results were relatively unaffected by the choice of the electrical head model, while the choice of the inverse method and source imaging package induced a considerable variability. In particular, a relatively strong difference was found between LCMV beamformer solutions on one hand and eLORETA/WMNE distributed inverse solutions on the other hand. We also observed a gradual decrease of consistency when results are compared between studies, within individual participants, and between individual participants. In order to provide reliable findings in the face of the observed variability, additional simulations involving interacting brain sources are required. Meanwhile, we encourage verification of the obtained results using more than one source imaging procedure.
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http://dx.doi.org/10.1016/j.neuroimage.2017.02.076DOI Listing
May 2017

SEEG assistant: a 3DSlicer extension to support epilepsy surgery.

BMC Bioinformatics 2017 Feb 23;18(1):124. Epub 2017 Feb 23.

"Claudio Munari" Center for Epilepsy Surgery, Niguarda Hospital, Milan, Italy.

Background: In the evaluation of Stereo-Electroencephalography (SEEG) signals, the physicist's workflow involves several operations, including determining the position of individual electrode contacts in terms of both relationship to grey or white matter and location in specific brain regions. These operations are (i) generally carried out manually by experts with limited computer support, (ii) hugely time consuming, and (iii) often inaccurate, incomplete, and prone to errors.

Results: In this paper we present SEEG Assistant, a set of tools integrated in a single 3DSlicer extension, which aims to assist neurosurgeons in the analysis of post-implant structural data and hence aid the neurophysiologist in the interpretation of SEEG data. SEEG Assistant consists of (i) a module to localize the electrode contact positions using imaging data from a thresholded post-implant CT, (ii) a module to determine the most probable cerebral location of the recorded activity, and (iii) a module to compute the Grey Matter Proximity Index, i.e. the distance of each contact from the cerebral cortex, in order to discriminate between white and grey matter location of contacts. Finally, exploiting 3DSlicer capabilities, SEEG Assistant offers a Graphical User Interface that simplifies the interaction between the user and the tools. SEEG Assistant has been tested on 40 patients segmenting 555 electrodes, and it has been used to identify the neuroanatomical loci and to compute the distance to the nearest cerebral cortex for 9626 contacts. We also performed manual segmentation and compared the results between the proposed tool and gold-standard clinical practice. As a result, the use of SEEG Assistant decreases the post implant processing time by more than 2 orders of magnitude, improves the quality of results and decreases, if not eliminates, errors in post implant processing.

Conclusions: The SEEG Assistant Framework for the first time supports physicists by providing a set of open-source tools for post-implant processing of SEEG data. Furthermore, SEEG Assistant has been integrated into 3D Slicer, a software platform for the analysis and visualization of medical images, overcoming limitations of command-line tools.
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http://dx.doi.org/10.1186/s12859-017-1545-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5324222PMC
February 2017

Distinctive neuronal firing patterns in subterritories of the subthalamic nucleus.

Clin Neurophysiol 2016 Nov 10;127(11):3387-3393. Epub 2016 Sep 10.

Department of Neurology of the University Hospital Wuerzburg and Julius-Maximilians-University, 97080 Wuerzburg, Germany.

Objective: Deep brain stimulation of the subthalamic nucleus (STN-DBS) is an established treatment for Parkinson's disease (PD). Anatomical connectivity analyses and task-related physiological studies have divided the STN into different functional domains: sensorimotor, limbic, and associative - located in its dorsolateral (dSTN), anteroventral (vSTN) and medial territories, respectively. Targeting sensorimotor STN is essential for stimulation efficacy and is supported by intraoperative micro-electrode recordings. A different neuronal signature in microelectrode recordings across STN subterritories was explored in this study.

Methods: Stable recordings from 30 PD patients were assigned to dSTN or vSTN by means of an anatomical method (based on fused computed tomography/magnetic resonance images) and through a priori tri-segmented partition of the recording itself. We computed the inter-spike interval (ISI) and ISI-characteristics, mean firing rate (MFR), discharge patterns and mean burst rate (MBR) of each detected single unit activity.

Results: We showed a different MBR between dSTN and vSTN (1.51±0.18 vs. 1.76±0.22events/minute, Wilcoxon rank sum test, p<0.05) and a trend in the difference between their MFR (12.78 vs. 15.05Hz, Wilcoxon rank sum test, p=0.053) only with the anatomically based method.

Conclusion: Burst firing differs across STN subterritories.

Significance: Different functions of subthalamic domains might be reflected by distinctive burst signalling of its subterritories.
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http://dx.doi.org/10.1016/j.clinph.2016.09.004DOI Listing
November 2016

Microenvironment complexity and matrix stiffness regulate breast cancer cell activity in a 3D in vitro model.

Sci Rep 2016 10 13;6:35367. Epub 2016 Oct 13.

National Council of Research (CNR) - IEIIT Institute, Genoa, 16149, Italy.

Three-dimensional (3D) cell cultures represent fundamental tools for the comprehension of cellular phenomena both in normal and in pathological conditions. In particular, mechanical and chemical stimuli play a relevant role on cell fate, cancer onset and malignant evolution. Here, we use mechanically-tuned alginate hydrogels to study the role of substrate elasticity on breast adenocarcinoma cell activity. The hydrogel elastic modulus (E) was measured via atomic force microscopy (AFM) and a remarkable range (150-4000 kPa) was obtained. A breast cancer cell line, MCF-7, was seeded within the 3D gels, on standard Petri and alginate-coated dishes (2D controls). Cells showed dramatic morphological differences when cultured in 3D versus 2D, exhibiting a flat shape in both 2D conditions, while maintaining a circular, spheroid-organized (cluster) conformation within the gels, similar to those in vivo. Moreover, we observed a strict correlation between cell viability and substrate elasticity; in particular, the number of MCF-7 cells decreased constantly with increasing hydrogel elasticity. Remarkably, the highest cellular proliferation rate, associated with the formation of cell clusters, occurred at two weeks only in the softest hydrogels (E = 150-200 kPa), highlighting the need to adopt more realistic and a priori defined models for in vitro cancer studies.
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http://dx.doi.org/10.1038/srep35367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062115PMC
October 2016

Automatic segmentation of deep intracerebral electrodes in computed tomography scans.

BMC Bioinformatics 2015 Mar 25;16:99. Epub 2015 Mar 25.

Neuroscience Center, University of Helsinki, P.O. Box 56 (Viikinkaari 4) FI-00014, Helsinki, Finland.

Background: Invasive monitoring of brain activity by means of intracerebral electrodes is widely practiced to improve pre-surgical seizure onset zone localization in patients with medically refractory seizures. Stereo-Electroencephalography (SEEG) is mainly used to localize the epileptogenic zone and a precise knowledge of the location of the electrodes is expected to facilitate the recordings interpretation and the planning of resective surgery. However, the localization of intracerebral electrodes on post-implant acquisitions is usually time-consuming (i.e., manual segmentation), it requires advanced 3D visualization tools, and it needs the supervision of trained medical doctors in order to minimize the errors. In this paper we propose an automated segmentation algorithm specifically designed to segment SEEG contacts from a thresholded post-implant Cone-Beam CT volume (0.4 mm, 0.4 mm, 0.8 mm). The algorithm relies on the planned position of target and entry points for each electrode as a first estimation of electrode axis. We implemented the proposed algorithm into DEETO, an open source C++ prototype based on ITK library.

Results: We tested our implementation on a cohort of 28 subjects in total. The experimental analysis, carried out over a subset of 12 subjects (35 multilead electrodes; 200 contacts) manually segmented by experts, show that the algorithm: (i) is faster than manual segmentation (i.e., less than 1s/subject versus a few hours) (ii) is reliable, with an error of 0.5 mm ± 0.06 mm, and (iii) it accurately maps SEEG implants to their anatomical regions improving the interpretability of electrophysiological traces for both clinical and research studies. Moreover, using the 28-subject cohort we show here that the algorithm is also robust (error < 0.005 mm) against deep-brain displacements (< 12 mm) of the implanted electrode shaft from those planned before surgery.

Conclusions: Our method represents, to the best of our knowledge, the first automatic algorithm for the segmentation of SEEG electrodes. The method can be used to accurately identify the neuroanatomical loci of SEEG electrode contacts by a non-expert in a fast and reliable manner.
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http://dx.doi.org/10.1186/s12859-015-0511-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393625PMC
March 2015

A digital repository with an extensible data model for biobanking and genomic analysis management.

BMC Genomics 2014 6;15 Suppl 3:S3. Epub 2014 May 6.

Motivation: Molecular biology laboratories require extensive metadata to improve data collection and analysis. The heterogeneity of the collected metadata grows as research is evolving in to international multi-disciplinary collaborations and increasing data sharing among institutions. Single standardization is not feasible and it becomes crucial to develop digital repositories with flexible and extensible data models, as in the case of modern integrated biobanks management.

Results: We developed a novel data model in JSON format to describe heterogeneous data in a generic biomedical science scenario. The model is built on two hierarchical entities: processes and events, roughly corresponding to research studies and analysis steps within a single study. A number of sequential events can be grouped in a process building up a hierarchical structure to track patient and sample history. Each event can produce new data. Data is described by a set of user-defined metadata, and may have one or more associated files. We integrated the model in a web based digital repository with a data grid storage to manage large data sets located in geographically distinct areas. We built a graphical interface that allows authorized users to define new data types dynamically, according to their requirements. Operators compose queries on metadata fields using a flexible search interface and run them on the database and on the grid. We applied the digital repository to the integrated management of samples, patients and medical history in the BIT-Gaslini biobank. The platform currently manages 1800 samples of over 900 patients. Microarray data from 150 analyses are stored on the grid storage and replicated on two physical resources for preservation. The system is equipped with data integration capabilities with other biobanks for worldwide information sharing.

Conclusions: Our data model enables users to continuously define flexible, ad hoc, and loosely structured metadata, for information sharing in specific research projects and purposes. This approach can improve sensitively interdisciplinary research collaboration and allows to track patients' clinical records, sample management information, and genomic data. The web interface allows the operators to easily manage, query, and annotate the files, without dealing with the technicalities of the data grid.
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http://dx.doi.org/10.1186/1471-2164-15-S3-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4083403PMC
March 2015

A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience.

BMC Med Inform Decis Mak 2012 Oct 8;12:115. Epub 2012 Oct 8.

University of Genoa, Dept. of Computer Science, Bioengineering, Robotics and Systems Engineering, Genoa, Italy.

Background: Robust, extensible and distributed databases integrating clinical, imaging and molecular data represent a substantial challenge for modern neuroscience. It is even more difficult to provide extensible software environments able to effectively target the rapidly changing data requirements and structures of research experiments. There is an increasing request from the neuroscience community for software tools addressing technical challenges about: (i) supporting researchers in the medical field to carry out data analysis using integrated bioinformatics services and tools; (ii) handling multimodal/multiscale data and metadata, enabling the injection of several different data types according to structured schemas; (iii) providing high extensibility, in order to address different requirements deriving from a large variety of applications simply through a user runtime configuration.

Methods: A dynamically extensible data structure supporting collaborative multidisciplinary research projects in neuroscience has been defined and implemented. We have considered extensibility issues from two different points of view. First, the improvement of data flexibility has been taken into account. This has been done through the development of a methodology for the dynamic creation and use of data types and related metadata, based on the definition of "meta" data model. This way, users are not constrainted to a set of predefined data and the model can be easily extensible and applicable to different contexts. Second, users have been enabled to easily customize and extend the experimental procedures in order to track each step of acquisition or analysis. This has been achieved through a process-event data structure, a multipurpose taxonomic schema composed by two generic main objects: events and processes. Then, a repository has been built based on such data model and structure, and deployed on distributed resources thanks to a Grid-based approach. Finally, data integration aspects have been addressed by providing the repository application with an efficient dynamic interface designed to enable the user to both easily query the data depending on defined datatypes and view all the data of every patient in an integrated and simple way.

Results: The results of our work have been twofold. First, a dynamically extensible data model has been implemented and tested based on a "meta" data-model enabling users to define their own data types independently from the application context. This data model has allowed users to dynamically include additional data types without the need of rebuilding the underlying database. Then a complex process-event data structure has been built, based on this data model, describing patient-centered diagnostic processes and merging information from data and metadata. Second, a repository implementing such a data structure has been deployed on a distributed Data Grid in order to provide scalability both in terms of data input and data storage and to exploit distributed data and computational approaches in order to share resources more efficiently. Moreover, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications.

Conclusions: Based on such repository, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications.
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http://dx.doi.org/10.1186/1472-6947-12-115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3560115PMC
October 2012

Metabotropic γ-aminobutyric acid (GABAB) receptors modulate feeding behavior in the calcisponge Leucandra aspera.

J Exp Zool A Ecol Genet Physiol 2011 Mar 8;315(3):132-40. Epub 2010 Dec 8.

Dipartimento per lo Studio del Territorio e delle sue Risorse (DIPTERIS), Università di Genova, Genova, Italy.

Here, we report the presence of the γ-aminobutyric acid (GABA)-ergic system in the calcisponge Leucandra aspera and examine the cellular localization of the components of this system, including GABA-like receptors using immunofluorescence and confocal microscopy. Furthermore, we demonstrate for the first time that GABA plays a functional role as a messenger in regulating sponge-feeding behavior. We found that both GABA(B) R1 and R2 subunits are present in the choanocytes of sponges as well as in the eso- and endopinacocytes. The functional role of GABA in the feeding behavior of this sponge was tested. The involvement of GABA receptors in the endocytic processes in L. aspera was demonstrated with dextran conjugated to Texas Red as a marker for material ingestion and by treating isolated sponge cells with a GABA(B) receptor agonist and an antagonist. The amount of dextran that was ingested increased in dissociated sponge cells when the GABA(B) receptor agonist baclofen was used, and this stimulatory effect was prevented by treatment with the GABA(B) receptor antagonist phaclofen. The baclofen effect on uptake was blocked by treatment with pertussis toxin, thus indicating a role for G proteins in modulating feeding behavior in L. aspera. Moreover, we found evidence that GABA receptors are involved in the consumption of dissolved organic matter by sponge cells. These findings suggest that GABA receptors and their functional role are highly conservative traits in the animal kingdom prenervous system evolution.
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http://dx.doi.org/10.1002/jez.657DOI Listing
March 2011

Grid-distributed statistical parametric mapping of SPECT and PET neuroimages.

Neuroinformatics 2011 Mar;9(1):85-90

IBFM-CNR, University of Milan-Bicocca, H S. Raffaele Institute, via F.lli Cervi 93, 20090, Segrate, MI, Italy.

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http://dx.doi.org/10.1007/s12021-010-9089-3DOI Listing
March 2011

A three-dimensional traction/torsion bioreactor system for tissue engineering.

Int J Artif Organs 2010 Jun;33(6):362-9

Advanced Biotechnology Center (CBA), Genoa, Italy.

Purpose: The aim of this study was to design, develop and validate a simple, compact bioreactor system for tissue engineering. The resulting bioreactor was designed to achieve ease-of-use and low costs for automated cell-culturing procedures onto three-dimensional scaffolds under controlled torsion/traction regimes.

Methods: Highly porous poly-caprolactone-based scaffolds were used as substrates colonized by fibroblast cells (3T3 cell line). Constructs were placed within the cylindrical culture chamber, clumped at the ends and exposed to controlled sequences of torsional stimuli (forward/back-forward sequential cycles of 100 degrees from neutral position at a rate of 600 degrees/min) through a stepper-motor; working settings were defined via PC by an easy user-interface. Cell adhesion, morphology, cytoskeletal fiber orientation and gene expression of extracellular matrix proteins (collagen type I, tenascin C, collagen type III) were evaluated after three days of torsional stimulation in the bioreactor system.

Results And Conclusions: The 3D bioreactor system was validated in terms of sterility, experimental reproducibility and flexibility. Cells adhered well onto the polymeric scaffolds. Collagen type I, tenascin C and collagen type III gene expression were significantly up-regulated when cells were cultured under torsion in the bioreactor for three days. In conclusion, we have developed a simple, efficient and versatile 3D cell-culture system to engineer ligament grafts. This system can be used either as a model to investigate mechanisms of tissue development or as a graft manufacturing system for possible clinical use in the field of regenerative medicine.
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June 2010

Survival Online: a web-based service for the analysis of correlations between gene expression and clinical and follow-up data.

BMC Bioinformatics 2009 Oct 15;10 Suppl 12:S10. Epub 2009 Oct 15.

University of Genoa, Department of Communication, Computer and System Sciences, Viale Causa 13, Genoa, Italy.

Background: Complex microarray gene expression datasets can be used for many independent analyses and are particularly interesting for the validation of potential biomarkers and multi-gene classifiers. This article presents a novel method to perform correlations between microarray gene expression data and clinico-pathological data through a combination of available and newly developed processing tools.

Results: We developed Survival Online (available at http://ada.dist.unige.it:8080/enginframe/bioinf/bioinf.xml), a Web-based system that allows for the analysis of Affymetrix GeneChip microarrays by using a parallel version of dChip. The user is first enabled to select pre-loaded datasets or single samples thereof, as well as single genes or lists of genes. Expression values of selected genes are then correlated with sample annotation data by uni- or multi-variate Cox regression and survival analyses. The system was tested using publicly available breast cancer datasets and GO (Gene Ontology) derived gene lists or single genes for survival analyses.

Conclusion: The system can be used by bio-medical researchers without specific computation skills to validate potential biomarkers or multi-gene classifiers. The design of the service, the parallelization of pre-processing tasks and the implementation on an HPC (High Performance Computing) environment make this system a useful tool for validation on several independent datasets.
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http://dx.doi.org/10.1186/1471-2105-10-S12-S10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2762059PMC
October 2009

XTENS - an eXTensible environment for neuroscience.

Stud Health Technol Inform 2009 ;147:127-36

Department of Communication, System and Computer Science, University of Genoa, Italy.

The XTENS (eXTensible Environment for NeuroScience) platform consists in an highly extensible environment for collaborative work that improve repeatability of experiment and provides data storage and analysis capabilities. The platform is divided in repository and application domains, branched in services with different purpose. The first domain is the central component of the platform and consists in a multimodal repository with a client-server architecture. The second one provides remote tools for image and signal visualization and analysis. The main issue for such a platform is not only to provide an extensible collaborative environment, but also to build a development platform for testing models and algorithms in neuroscience. For these reasons a Grid approach has been considered. Both computational and data Grids infrastructures can be exploited to analyze and share large datasets of distributed data. The architecture has been deployed to support surgical planning for patients affected by drug resistant epilepsy. In that scenario, a complex analysis for a fully multimodal dataset including different image modalities, EEG and video is required to localize the origin of the ictal discharge and critical brain areas. As first results, prototype versions of both repository and application domain components are presented.
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September 2009

A model to prioritize access to elective surgery on the basis of clinical urgency and waiting time.

BMC Health Serv Res 2009 Jan 1;9. Epub 2009 Jan 1.

Health Management Unit, S. Martino University Hospital, L.go R. Benzi 10, 16132 Genoa, Italy.

Background: Prioritization of waiting lists for elective surgery represents a major issue in public systems in view of the fact that patients often suffer from consequences of long waiting times. In addition, administrative and standardized data on waiting lists are generally lacking in Italy, where no detailed national reports are available. This is true although since 2002 the National Government has defined implicit Urgency-Related Groups (URGs) associated with Maximum Time Before Treatment (MTBT), similar to the Australian classification. The aim of this paper is to propose a model to manage waiting lists and prioritize admissions to elective surgery.

Methods: In 2001, the Italian Ministry of Health funded the Surgical Waiting List Info System (SWALIS) project, with the aim of experimenting solutions for managing elective surgery waiting lists. The project was split into two phases. In the first project phase, ten surgical units in the largest hospital of the Liguria Region were involved in the design of a pre-admission process model. The model was embedded in a Web based software, adopting Italian URGs with minor modifications. The SWALIS pre-admission process was based on the following steps: 1) urgency assessment into URGs; 2) correspondent assignment of a pre-set MTBT; 3) real time prioritization of every referral on the list, according to urgency and waiting time. In the second project phase a prospective descriptive study was performed, when a single general surgery unit was selected as the deployment and test bed, managing all registrations from March 2004 to March 2007 (1809 ordinary and 597 day cases). From August 2005, once the SWALIS model had been modified, waiting lists were monitored and analyzed, measuring the impact of the model by a set of performance indexes (average waiting time, length of the waiting list) and Appropriate Performance Index (API).

Results: The SWALIS pre-admission model was used for all registrations in the test period, fully covering the case mix of the patients referred to surgery. The software produced real time data and advanced parameters, providing patients and users useful tools to manage waiting lists and to schedule hospital admissions with ease and efficiency. The model protected patients from horizontal and vertical inequities, while positive changes in API were observed in the latest period, meaning that more patients were treated within their MTBT.

Conclusion: The SWALIS model achieves the purpose of providing useful data to monitor waiting lists appropriately. It allows homogeneous and standardized prioritization, enhancing transparency, efficiency and equity. Due to its applicability, it might represent a pragmatic approach towards surgical waiting lists, useful in both clinical practice and strategic resource management.
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http://dx.doi.org/10.1186/1472-6963-9-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651867PMC
January 2009

A Web-based and Grid-enabled dChip version for the analysis of large sets of gene expression data.

BMC Bioinformatics 2008 Nov 13;9:480. Epub 2008 Nov 13.

Computer Science, Systems, and Communication Department, University of Genova, Viale Causa 12, Genova, Italy.

Background: Microarray techniques are one of the main methods used to investigate thousands of gene expression profiles for enlightening complex biological processes responsible for serious diseases, with a great scientific impact and a wide application area. Several standalone applications had been developed in order to analyze microarray data. Two of the most known free analysis software packages are the R-based Bioconductor and dChip. The part of dChip software concerning the calculation and the analysis of gene expression has been modified to permit its execution on both cluster environments (supercomputers) and Grid infrastructures (distributed computing).This work is not aimed at replacing existing tools, but it provides researchers with a method to analyze large datasets without any hardware or software constraints.

Results: An application able to perform the computation and the analysis of gene expression on large datasets has been developed using algorithms provided by dChip. Different tests have been carried out in order to validate the results and to compare the performances obtained on different infrastructures. Validation tests have been performed using a small dataset related to the comparison of HUVEC (Human Umbilical Vein Endothelial Cells) and Fibroblasts, derived from same donors, treated with IFN-alpha.Moreover performance tests have been executed just to compare performances on different environments using a large dataset including about 1000 samples related to Breast Cancer patients.

Conclusion: A Grid-enabled software application for the analysis of large Microarray datasets has been proposed. DChip software has been ported on Linux platform and modified, using appropriate parallelization strategies, to permit its execution on both cluster environments and Grid infrastructures. The added value provided by the use of Grid technologies is the possibility to exploit both computational and data Grid infrastructures to analyze large datasets of distributed data. The software has been validated and performances on cluster and Grid environments have been compared obtaining quite good scalability results.
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http://dx.doi.org/10.1186/1471-2105-9-480DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596147PMC
November 2008

Hydroxyapatite-coated polycaprolacton wide mesh as a model of open structure for bone regeneration.

Tissue Eng Part A 2009 Jan;15(1):155-63

Department of Informatics, Systemistics and Telematics (DIST), University of Genoa, Genoa, Italy.

In principle, three-dimensional (3D) osteoconductive grafts with a proper chemical composition, high total porosity, and fully interconnected pores are suitable carriers to provide a proper substrate for in vivo neobone tissue ingrowth. However, most porous materials carry some intrinsic limits because of their internal structure (i.e., limited macroporosity and small pore interconnection size), representing a physical constraint for a massive blood afflux and bone ingrowth and therefore for generating effective osteopermissive grafts. We therefore hypothesized that an unconventional scaffold, based on an "open-structure" concept, should not pose any limit to vascularization of grafts and consequently to the amount of bone growth. Starting from this hypothesis, we have designed and developed a 3D osteoconductive polymeric-based wide-net mesh. Polymer fibers, joining hydroxyapatite beads, were coated with a thin layer of calcium phosphate (Ca-P), coupling the osteoconductivity properties of Ca-P with the handness and bulk properties of polymers. This completely open 3D scaffold prototype was tested both in vitro and in vivo, displaying a promising in vivo blood vessel invasion and bone-forming efficiency.
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http://dx.doi.org/10.1089/ten.tea.2007.0410DOI Listing
January 2009

Effect of the bioactive metabolite euplotin C on phagocytosis and fluid-phase endocytosis in the single-celled eukaryote Paramecium.

Aquat Toxicol 2007 Nov 12;85(1):67-75. Epub 2007 Aug 12.

Dipartimento per lo Studio del Territorio e delle sue Risorse (DIP.TE.RIS.), Università di Genova, Corso Europa 26, I-16132, Genova, Italy.

The effect of euplotin C -- a lipophilic bioactive metabolite produced by the ciliate Euplotes crassus -- on the kinetics of both phagocytosis of latex particles and fluid-phase uptake of dextran, was studied in the single-cell ciliate Paramecium primaurelia. The inhibition of food vacuole formation was concentration- and time-dependent (p<0.001), even if euplotin C did not completely block the phagocytosis. Following a 15 min treatment with a euplotin C (0.5 microg/ml), the latex particle uptake was inhibited up to 25%. Furthermore, the pretreatment of cells with taxol strongly counteracted euplotin C effect. The amount of extracellularly provided dextran, which is internalized exclusively by fluid-phase uptake, was quantified in cells whose phagocytic activity was blocked by trifluoperazine. The amount of the internalized dextran was about 50% of that in controls after 15 min incubation in the presence of euplotin C. Fluorescence confocal images showed that no endosomes were formed on the surface of these cells. The effect of euplotin C on the food vacuole formation and fluid-phase endocytosis is apparently mediated by a modification of microtubule network.
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http://dx.doi.org/10.1016/j.aquatox.2007.08.001DOI Listing
November 2007

The GABAergic-like system in the marine demosponge Chondrilla nucula.

Microsc Res Tech 2007 Nov;70(11):944-51

Department for the Study of the Territory and its Resources, University of Genoa, 16132 Genova, Italy.

Gamma-amino butyric acid (GABA) is believed to be the principal inhibitory neurotransmitter in the mammalian central nervous system, a function that has been extended to a number of invertebrate systems. The presence of GABA in the marine demosponge Chondrilla nucula was verified using immunofluorescence detection and high-pressure liquid chromatography. A strong GABA-like immunoreactivity (IR) was found associated with choanocytes, exopinacocytes, endopinacocytes lining inhalant, and exhalant canals, as well as in archaeocytes scattered in the mesohyl. The capacity to synthesize GABA from glutamate and to transport it into the vesicles was confirmed by the presence in C. nucula of glutamate decarboxylase (GAD) and vesicular GABA transporters (vGATs), respectively. GAD-like and vGAT-like IR show the same distribution as GABA-like IR. Supporting the similarity between sponge and mammalian proteins, bands with an apparent molecular weight of about 65-67 kDa and 57 kDa were detected using antibodies raised against mammalian GAD and vGAT, respectively. A functional metabotropic GABA(B)-like receptor is also present in C. nucula. Indeed, both GABA(B) R1 and R2 isoforms were detected by immunoblot and immunofluorescence. Also in this case, IR was found in choanocytes, exopinacocytes, and endopinacocytes. The content of GABA in C. nucula amounts to 1225.75 +/- 79 pmol/mg proteins and GABA is released into the medium when sponge cells are depolarized. In conclusion, this study is the first indication of the existence of the GABA biosynthetic enzyme GAD and of the GABA transporter vGAT in sponges, as well as the first demonstration that the neurotransmitter GABA is released extracellularly.
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http://dx.doi.org/10.1002/jemt.20499DOI Listing
November 2007

A Grid-based solution for management and analysis of microarrays in distributed experiments.

BMC Bioinformatics 2007 Mar 8;8 Suppl 1:S7. Epub 2007 Mar 8.

Computer Science, Systems, and Communication Department, University of Genova, Viale Causa 12, 16100 Genova, Italy.

Several systems have been presented in the last years in order to manage the complexity of large microarray experiments. Although good results have been achieved, most systems tend to lack in one or more fields. A Grid based approach may provide a shared, standardized and reliable solution for storage and analysis of biological data, in order to maximize the results of experimental efforts. A Grid framework has been therefore adopted due to the necessity of remotely accessing large amounts of distributed data as well as to scale computational performances for terabyte datasets. Two different biological studies have been planned in order to highlight the benefits that can emerge from our Grid based platform. The described environment relies on storage services and computational services provided by the gLite Grid middleware. The Grid environment is also able to exploit the added value of metadata in order to let users better classify and search experiments. A state-of-art Grid portal has been implemented in order to hide the complexity of framework from end users and to make them able to easily access available services and data. The functional architecture of the portal is described. As a first test of the system performances, a gene expression analysis has been performed on a dataset of Affymetrix GeneChip Rat Expression Array RAE230A, from the ArrayExpress database. The sequence of analysis includes three steps: (i) group opening and image set uploading, (ii) normalization, and (iii) model based gene expression (based on PM/MM difference model). Two different Linux versions (sequential and parallel) of the dChip software have been developed to implement the analysis and have been tested on a cluster. From results, it emerges that the parallelization of the analysis process and the execution of parallel jobs on distributed computational resources actually improve the performances. Moreover, the Grid environment have been tested both against the possibility of uploading and accessing distributed datasets through the Grid middleware and against its ability in managing the execution of jobs on distributed computational resources. Results from the Grid test will be discussed in a further paper.
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http://dx.doi.org/10.1186/1471-2105-8-S1-S7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1885859PMC
March 2007

Gamma-aminobutyric acid and related molecules in the sea fan Eunicella cavolini (Cnidaria: Octocorallia): a biochemical and immunohistochemical approach.

Cell Tissue Res 2007 Jul 12;329(1):187-96. Epub 2007 Apr 12.

Dipartimento Biologia, Università di Genova, Genoa, Italy.

The aim of this study has been the biochemical demonstration of the presence of gamma-aminobutyric acid (GABA) in the Mediterranean sea fan Eunicella cavolini by means of high-performance liquid chromatography, and the description of the distribution pattern of GABA and its related molecules, glutamic acid decarboxylase (GAD), vesicular GABA transporter (VGAT) and one of the GABA receptors (GABA(B) R) by immunohistochemical methods. The interrelationships of GABA, GAD and GABA receptor immunoreactivity have been established by using double-immunohistochemical methods and confocal microscopy. The immunodetection of monoclonal and/or polyclonal antibodies has revealed GABA immunoreactivity throughout the polyp tissue, both in neuronal and non-neuronal elements. GAD immunoreactivity has been mostly localized in the neuronal compartment, contacting epithelial and muscular elements. GABA(B) R immunoreactivity appears particularly intense in the nematocytes and in the oocyte envelope; its presence in GAD-immunoreactive neurons in the tentacles suggests an autocrine type of regulation. Western blot analysis has confirmed that a GABA(B) R, with a molecular weight of 142 kDa, similar to that of rat brain, is present in E. cavolini polyp tissue. The identification of the sites of the synthesis, vesicular transport, storage and reception of GABA strongly suggests the presence of an almost complete set of GABA-related molecules for the functioning of the GABAergic system in this simple nervous system. The distribution of these different immunoreactivities has allowed us to hypothesize GABA involvement in nematocyst discharge, in body wall and enteric muscular contraction, in neuronal integration and in male gametocyte differentiation.
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http://dx.doi.org/10.1007/s00441-007-0408-4DOI Listing
July 2007

Endocytosis of GABAB receptors modulates membrane excitability in the single-celled organism Paramecium.

J Cell Sci 2006 May 25;119(Pt 10):2056-64. Epub 2006 Apr 25.

Department for the Study of the Territory and its Resources (DIP.TE.RIS.), University of Genoa, Corso Europa 26, 16132 Genova, Italy.

GABAB receptors modulate swimming behavior in Paramecium by inhibiting dihydropyridine-sensitive Ca2+ channels via G-proteins. Prolonged occupancy of GABAB receptors by baclofen results in a decrease in GABAB receptor functions. Since changes in the number of cell-surface GABAA receptors have been postulated to be of importance in modulating inhibitory synaptic transmission in neurons, we have studied the cell-surface expression and maintenance of GABAB receptors in P. primaurelia. In this study, we use immunostaining in electron and confocal microscopy to demonstrate that constitutive internalization of GABAB receptors in P. primaurelia is mediated by clathrin-dependent and -independent endocytosis. Indeed, GABAB receptors colocalize with the adaptin complex AP2, which is implicated in the selective recruitment of integral membrane proteins to clathrin-coated vesicles, and with caveolin 1, which is associated with uncoated membrane invaginations. Furthermore, when endocytosis is blocked with hypertonic medium, cytosol acidification, filipin or with a peptide that disrupts the association between amphiphysin and dynamin, the effect of baclofen on swimming is increased. These results suggest that GABAB receptor endocytosis into clathrin-coated and -uncoated vesicles represents an important mechanism in the modulation of swimming behavior in Paramecium.
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http://dx.doi.org/10.1242/jcs.02931DOI Listing
May 2006

GABAB receptor intracellular trafficking after internalization in Paramecium.

Microsc Res Tech 2005 Dec;68(5):290-5

Department for the Study of Territory and its Resources (DIP.TE.RIS.), University of Genoa, 16132 Genoa, Italy.

The number of neurotransmitter receptors on the plasma membrane is regulated by the traffic of intracellular vesicles. Golgi-derived vesicles provide newly synthesized receptors to the cell surface, whereas clathrin-coated vesicles are the initial vehicles for sequestration of surface receptors, which are ultimately degraded or recycled. We have previously shown that GABAB receptors display a punctuate vesicular pattern dispersed on the cell surface and throughout the cytoplasm and are internalized via clathrin-dependent and -independent endocytosis. Here we have studied constitutive GABAB receptor trafficking after internalization in Paramecium primaurelia by confocal laser scanning microscopy and multiple immunofluorescence analysis. After internalization, receptors are targeted to the early endosomes characterized by the molecular markers EEA1 and rab5. Some of these receptors, destined for recycling back to the plasma membrane, traffic from the early endosomes to the endosomal recycling compartment that is characterized by the presence of rab4-immunoreactivity (IR). Receptors that are destined for degradation exit the endosomal pathway at the early endosomes and traffic to the late endosome-lysosome pathway. In fact, some of the GABAB-positive compartments were identified as lysosomal structures by double staining with the lysosomal marker LAMP-1. GABAB vesicle structures also colocalize with TGN38-IR and rab11-IR. TGN38 and rab11 are proteins found in association with post-Golgi and recycling endosomes, respectively.
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http://dx.doi.org/10.1002/jemt.20250DOI Listing
December 2005

Simulation of the biomechanical behavior of the skin in virtual surgical applications by finite element method.

IEEE Trans Biomed Eng 2005 Sep;52(9):1514-21

Department of Communication, Computer and System Sciences, University of Genoa, 16145 Genoa, Italy.

The objective of this study was to develop a software application that is able to support plastic surgeons interested in applying simulations and soft tissue modeling during presurgical planning activities. By using our user-friendly interface and force-displacement graphs, users can analyze scalp skin behaviors when subjected to stress. Users can 1) determine the dynamic of a general point of scalp skin after the application of a specific force, 2) predict the force needed for displacement of a point, and 3) study the deformation of all the points of the entire scalp based on the force applied. Results showed how users are able to manipulate and analyze mechanical behaviors on a mechanical model rather than on a pure geometric qualitative physiological model. The entire application was developed on a Silicon Graphics workstation.
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http://dx.doi.org/10.1109/TBME.2005.851529DOI Listing
September 2005