Publications by authors named "Monica Santamaria"

49 Publications

ITSoneWB: profiling global taxonomic diversity of eukaryotic communities on Galaxy.

Bioinformatics 2021 Jun 12. Epub 2021 Jun 12.

Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari 70126, Italy.

Motivation: ITSoneWB (ITSone WorkBench) is a Galaxy-based bioinformatic environment where comprehensive and high-quality reference data are connected with established pipelines and new tools in an automated and easy-to-use service targeted at global taxonomic analysis of eukaryotic communities based on Internal Transcribed Spacer 1 variants high-throughput sequencing.

Availability: ITSoneWB has been deployed on the INFN-Bari ReCaS cloud facility and is freely available on the web at http://itsonewb.cloud.ba.infn.it/galaxy.

Supplementary Information: Supplementary data are available at https://github.com/ibiom-cnr/itsonewb/wiki.
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http://dx.doi.org/10.1093/bioinformatics/btab431DOI Listing
June 2021

Tuning of the Mg Alloy AZ31 Anodizing Process for Biodegradable Implants.

ACS Appl Mater Interfaces 2021 Mar 11;13(11):12866-12876. Epub 2021 Mar 11.

Dipartimento di Ingegneria, Università degli Studi di Palermo, Viale delle Scienze, Palermo 90128, Italy.

Coatings were grown on the AZ31 Mg alloy by a hard anodizing process in the hot glycerol phosphate-containing electrolyte. Anodizing conditions were optimized, maximizing corrosion resistance estimated by impedance measurements carried out in Hank's solution at 37 °C. A post anodizing annealing treatment (350 °C for 24 h) allowed us to further enhance the corrosion resistance of the coatings mainly containing magnesium phosphate according to energy-dispersive X-ray spectroscopy and Raman analyses. Gravimetric measurements revealed a hydrogen evolution rate within the limits acceptable for application of AZ31 in biomedical devices. tests demonstrated that the coatings are biocompatible with a preosteoblast cell line.
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http://dx.doi.org/10.1021/acsami.0c22933DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8041254PMC
March 2021

A Generalized Semiempirical Approach to the Modeling of the Optical Band Gap of Ternary Al-(Ga, Nb, Ta, W) Oxides Containing Different Alumina Polymorphs.

Inorg Chem 2021 Feb 20;60(3):1419-1435. Epub 2021 Jan 20.

Dipartimento di Ingegneria, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy.

A generalization of the modeling equation of optical band gap values for ternary oxides, as a function of cationic ratio composition, is carried out based on the semiempirical correlation between the differences in the electronegativity of oxygen and the average cationic electronegativity proposed some years ago. In this work, a novel approach is suggested to account for the differences in the band gap values of the different polymorphs of binary oxides as well as for ternary oxides existing in different crystalline structures. A preliminary test on the validity of the proposed modeling equations has been carried out by using the numerous experimental data pertaining to alumina and gallia polymorphs as well as the crystalline ternary GaAlO polymorphs (α-GaAlO and β-GaAlO) covering a large range of optical band gap values (4.50-8.50 eV). To make a more rigorous test of the modeling equation, we extended our investigation to amorphous ternary oxides anodically formed on Al-d-metal alloys (Al-Nb, Al-Ta, and Al-W) covering a large range of d-metal composition ( ≥ 0.2). In the last case, the novel approach allows one to overcome some difficulties experienced in fitting the optical band gap dependence from the Al-d-metal mixed anodic oxide composition as well as to provide a rationale for the departure, at the lowest d-metal content ( < 0.2), from the behavior observed for anodic films containing higher d-metal content.
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http://dx.doi.org/10.1021/acs.inorgchem.0c02691DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7877732PMC
February 2021

Graft infusion of adipose-derived mesenchymal stromal cells to prevent rejection in experimental intestinal transplantation: A feasibility study.

Clin Transplant 2021 04 5;35(4):e14226. Epub 2021 Feb 5.

TransplantChild ERN, Idipaz Institute, La Paz University Hospital, Madrid, Spain.

Background: Mesenchymal stromal cells (MSC) have been proposed as a promising complement to standard immunosuppression in solid organ transplantation because of their immunomodulatory properties. The present work addresses the role of adipose-derived MSC (Ad-MSC) in an experimental model of acute rejection in small bowel transplantation (SBT).

Material/methods: Heterotopic allogeneic SBT was performed. A single dose of 1.5x106 Ad-MSC was intra-arterially delivered just before graft reperfusion. Animals were divided into CONTROL (CTRL), CONTROL+Ad-MSC (CTRL_MSC), tacrolimus (TAC), and TAC+Ad-MSC (TAC_MSC) groups. Each Ad-MSC groups was subdivided in autologous and allogeneic third-party groups.

Results: Rejection rate and severity were similar in MSC-treated and untreated animals. CTRL_MSC animals showed a decrease in macrophages, T-cell (CD4, CD8, and Foxp3 subsets) and B-cell counts in the graft compared with CTRL, this decrease was attenuated in TAC_MSC animals. Pro- and anti-inflammatory cytokines and some chemokines and growth factors increased in CTRL_MSC animals, especially in the allogeneic group, whereas milder changes were seen in the TAC groups.

Conclusion: Ad-MSC did not prevent rejection when administered just before reperfusion. However, they showed immunomodulatory effects that could be relevant for a longer-term outcome. Interference between tacrolimus and the MSC effects should be addressed in further studies.
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http://dx.doi.org/10.1111/ctr.14226DOI Listing
April 2021

Communication Support Needs in Adults with Intellectual Disabilities and Its Relation to Quality of Life.

Int J Environ Res Public Health 2020 10 9;17(20). Epub 2020 Oct 9.

Institute for Community Inclusion (INICO), University of Salamanca, 37005 Salamanca, Spain.

Research suggests that individuals with intellectual disabilities (ID) experience difficulties in communication, ranging from intelligibility issues to more severe problems in the use and comprehension of spoken, written or sign language. Despite the negative effects that the inability to communicate have on quality of life (QoL), not much research has explored the relationship between communicative competence and QoL in the adult population with ID. The aim of this study was to describe the global communication profile of a sample of 281 adults with ID recruited from Grupo AMÁS Social Foundation, who differed in their level of communication support needs (CSN). The relationships between communicative competence and CSN with QoL were further examined. The results showed lower QoL indices for those participants characterized by their limited use of discourse and inability to exhibit certain communicative purposes, with the largest differences in the dimensions of self-determination, social inclusion, interpersonal relationships, emotional wellbeing and personal development. Overall, low levels of QoL were found for all participants, with even lower scores for the group identified as having CSN. A multiple regression model revealed that having speech/discourse competence is a powerful predictor of QoL, along with the level of disability and having the communicative competences to express likes and preferences or to establish new relationships. This clear relationship between communication and QoL is an important argument for disability support services when it comes to setting communication supports as a priority and as an important preventive step towards the protection of those at risk of exclusion.
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http://dx.doi.org/10.3390/ijerph17207370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7601275PMC
October 2020

DNA Multiple Sequence Alignment Guided by Protein Domains: The MSA-PAD 2.0 Method.

Methods Mol Biol 2018 ;1746:173-180

Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Bari, Italy.

Multiple sequence alignment (MSA) is a fundamental component in many DNA sequence analyses including metagenomics studies and phylogeny inference. When guided by protein profiles, DNA multiple alignments assume a higher precision and robustness. Here we present details of the use of the upgraded version of MSA-PAD (2.0), which is a DNA multiple sequence alignment framework able to align DNA sequences coding for single/multiple protein domains guided by PFAM or user-defined annotations. MSA-PAD has two alignment strategies, called "Gene" and "Genome," accounting for coding domains order and genomic rearrangements, respectively. Novel options were added to the present version, where the MSA can be guided by protein profiles provided by the user. This allows MSA-PAD 2.0 to run faster and to add custom protein profiles sometimes not present in PFAM database according to the user's interest. MSA-PAD 2.0 is currently freely available as a Web application at https://recasgateway.cloud.ba.infn.it/ .
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http://dx.doi.org/10.1007/978-1-4939-7683-6_13DOI Listing
February 2019

ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences.

Nucleic Acids Res 2018 01;46(D1):D127-D132

Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy.

A holistic understanding of environmental communities is the new challenge of metagenomics. Accordingly, the amplicon-based or metabarcoding approach, largely applied to investigate bacterial microbiomes, is moving to the eukaryotic world too. Indeed, the analysis of metabarcoding data may provide a comprehensive assessment of both bacterial and eukaryotic composition in a variety of environments, including human body. In this respect, whereas hypervariable regions of the 16S rRNA are the de facto standard barcode for bacteria, the Internal Transcribed Spacer 1 (ITS1) of ribosomal RNA gene cluster has shown a high potential in discriminating eukaryotes at deep taxonomic levels. As metabarcoding data analysis rely on the availability of a well-curated barcode reference resource, a comprehensive collection of ITS1 sequences supplied with robust taxonomies, is highly needed. To address this issue, we created ITSoneDB (available at http://itsonedb.cloud.ba.infn.it/) which in its current version hosts 985 240 ITS1 sequences spanning over 134 000 eukaryotic species. Each ITS1 is mapped on the NCBI reference taxonomy with its start and end positions precisely annotated. ITSoneDB has been developed in agreement to the FAIR guidelines by enabling the users to query and download its content through a simple web-interface and access relevant metadata by cross-linking to European Nucleotide Archive.
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http://dx.doi.org/10.1093/nar/gkx855DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753230PMC
January 2018

Electrochemical Tantalum Oxide for Resistive Switching Memories.

Adv Mater 2017 Nov 6;29(43). Epub 2017 Oct 6.

Institut für Werkstoffe der Elektrotechnik 2, RWTH Aachen University, 52074, Aachen, Germany.

Redox-based resistive switching memories (ReRAMs) are strongest candidates for the next-generation nonvolatile memories fulfilling the criteria for fast, energy efficient, and scalable green IT. These types of devices can also be used for selector elements, alternative logic circuits and computing, and memristive and neuromorphic operations. ReRAMs are composed of metal/solid electrolyte/metal junctions in which the solid electrolyte is typically a metal oxide or multilayer oxides structures. Here, this study offers an effective and cheap electrochemical approach to fabricate Ta/Ta O -based devices by anodizing. This method allows to grow high-quality and dense oxide thin films onto a metallic substrates with precise control over morphology and thickness. Electrochemical-oxide-based devices demonstrate superior properties, i.e., endurance of at least 10 pulse cycles and/or 10 I-V sweeps maintaining a good memory window with a low dispersion in R and R values, nanosecond fast switching, and data retention of at least 10 s. Multilevel programing capability is presented with both I-V sweeps and pulse measurements. Thus, it is shown that anodizing has a great prospective as a method for preparation of dense oxide films for resistive switching memories.
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http://dx.doi.org/10.1002/adma.201703357DOI Listing
November 2017

Diagnosis and predictors of sessile serrated adenoma after educational training in a large, community-based, integrated healthcare setting.

Gastrointest Endosc 2018 Mar 24;87(3):755-765.e1. Epub 2017 Aug 24.

Department of Gastroenterology, Kaiser Permanente Northern California, Walnut Creek, California, USA.

Background And Aims: Sessile serrated adenomas (SSAs) are precursors of 15% to 30% of colorectal cancers but are frequently underdiagnosed. We sought to measure the SSA detection rate (SDR) and predictors of SSA detection after educational training for community gastroenterologists and pathologists.

Methods: Colonoscopy and pathology data (2010-2014) from 3 medical centers at Kaiser Permanente Northern California were accessed electronically. Gastroenterologists and pathologists attended a training session on SSA diagnosis in 2012. Mean SDRs and patient-level predictors of SSA detection post-training (2013-2014) were investigated.

Results: Mean SDRs increased from .6% in 2010-2012 to 3.7% in 2013-2014. The increase in the detection of proximal SSAs was accompanied by a decrease in the detection of proximal hyperplastic polyps (HPs). Among 34,161 colonoscopies performed in 2013 to 2014, SDRs for screening, fecal immunochemical test positivity, surveillance, and diagnostic indication were 4.2%, 4.5%, 4.9%, and 3.0%, respectively. SSA detection was lower among Asians (adjusted odds ratio [aOR], .46; 95% confidence interval [CI], .31-.69) and Hispanics (aOR, .59; 95% CI, .36-.95) compared with non-Hispanic whites and higher among patients with synchronous conventional adenoma (aOR, 1.46; 95% CI, 1.15-1.86), HP (aOR, 1.74; 95% CI, 1.30-2.34), and current smokers (aOR, 1.78; 95% CI, 1.17-2.72). SDRs varied widely among experienced gastroenterologists, even after training (1.1%-8.1%). There was a moderately strong correlation between adenoma detection rate (ADR) and SDR for any SSA (r = .64, P = .0003) and for right-sided SSAs (r = .71, P < .0001).

Conclusions: Educational training significantly increased the detection of SSA, but a wide variation in SDR remained across gastroenterologists. SSA detection was inversely associated with Asian and Hispanic race/ethnicity and positively associated with the presence of conventional adenoma, HP, and current smoking. There was a moderately strong correlation between ADR and SDR.
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http://dx.doi.org/10.1016/j.gie.2017.08.012DOI Listing
March 2018

Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale.

Biol Rev Camb Philos Soc 2018 02 2;93(1):600-625. Epub 2017 Aug 2.

Global Biodiversity Information Facility Secretariat, Universitetsparken 15, 2100, København Ø, Denmark.

Much biodiversity data is collected worldwide, but it remains challenging to assemble the scattered knowledge for assessing biodiversity status and trends. The concept of Essential Biodiversity Variables (EBVs) was introduced to structure biodiversity monitoring globally, and to harmonize and standardize biodiversity data from disparate sources to capture a minimum set of critical variables required to study, report and manage biodiversity change. Here, we assess the challenges of a 'Big Data' approach to building global EBV data products across taxa and spatiotemporal scales, focusing on species distribution and abundance. The majority of currently available data on species distributions derives from incidentally reported observations or from surveys where presence-only or presence-absence data are sampled repeatedly with standardized protocols. Most abundance data come from opportunistic population counts or from population time series using standardized protocols (e.g. repeated surveys of the same population from single or multiple sites). Enormous complexity exists in integrating these heterogeneous, multi-source data sets across space, time, taxa and different sampling methods. Integration of such data into global EBV data products requires correcting biases introduced by imperfect detection and varying sampling effort, dealing with different spatial resolution and extents, harmonizing measurement units from different data sources or sampling methods, applying statistical tools and models for spatial inter- or extrapolation, and quantifying sources of uncertainty and errors in data and models. To support the development of EBVs by the Group on Earth Observations Biodiversity Observation Network (GEO BON), we identify 11 key workflow steps that will operationalize the process of building EBV data products within and across research infrastructures worldwide. These workflow steps take multiple sequential activities into account, including identification and aggregation of various raw data sources, data quality control, taxonomic name matching and statistical modelling of integrated data. We illustrate these steps with concrete examples from existing citizen science and professional monitoring projects, including eBird, the Tropical Ecology Assessment and Monitoring network, the Living Planet Index and the Baltic Sea zooplankton monitoring. The identified workflow steps are applicable to both terrestrial and aquatic systems and a broad range of spatial, temporal and taxonomic scales. They depend on clear, findable and accessible metadata, and we provide an overview of current data and metadata standards. Several challenges remain to be solved for building global EBV data products: (i) developing tools and models for combining heterogeneous, multi-source data sets and filling data gaps in geographic, temporal and taxonomic coverage, (ii) integrating emerging methods and technologies for data collection such as citizen science, sensor networks, DNA-based techniques and satellite remote sensing, (iii) solving major technical issues related to data product structure, data storage, execution of workflows and the production process/cycle as well as approaching technical interoperability among research infrastructures, (iv) allowing semantic interoperability by developing and adopting standards and tools for capturing consistent data and metadata, and (v) ensuring legal interoperability by endorsing open data or data that are free from restrictions on use, modification and sharing. Addressing these challenges is critical for biodiversity research and for assessing progress towards conservation policy targets and sustainable development goals.
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http://dx.doi.org/10.1111/brv.12359DOI Listing
February 2018

The metagenomic data life-cycle: standards and best practices.

Gigascience 2017 08;6(8):1-11

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.

Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonized way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (i) material sampling, (ii) material sequencing, (iii) data analysis, and (iv) data archiving and publishing. Taking examples from marine research, we summarize essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment. These aspects of metagenomics dataset generation have been to some extent addressed by the scientific community, but greater awareness and adoption is still needed. We emphasize the lack of standards relating to reporting how metagenomics datasets are analysed and how the metagenomics data analysis outputs should be archived and published. We propose best practice as a foundation for a community standard to enable reproducibility and better sharing of metagenomics datasets, leading ultimately to greater metagenomics data reuse and repurposing.
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http://dx.doi.org/10.1093/gigascience/gix047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737865PMC
August 2017

BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology.

BMC Ecol 2016 10 20;16(1):49. Epub 2016 Oct 20.

Fraunhofer Institute for Intelligent Analysis and Information Systems (IAIS), Schloss Birlinghoven, 53757, Sankt Augustin, Germany.

Background: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science. However, use of this approach in biodiversity science and ecology has thus far been quite limited.

Results: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible 'virtual laboratory', free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity.

Conclusions: Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.
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http://dx.doi.org/10.1186/s12898-016-0103-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5073428PMC
October 2016

Structural insight into the role of the Ton complex in energy transduction.

Nature 2016 Oct 21;538(7623):60-65. Epub 2016 Sep 21.

National Institute of Diabetes &Digestive &Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.

In Gram-negative bacteria, outer membrane transporters import nutrients by coupling to an inner membrane protein complex called the Ton complex. The Ton complex consists of TonB, ExbB, and ExbD, and uses the proton motive force at the inner membrane to transduce energy to the outer membrane via TonB. Here, we structurally characterize the Ton complex from Escherichia coli using X-ray crystallography, electron microscopy, double electron-electron resonance (DEER) spectroscopy, and crosslinking. Our results reveal a stoichiometry consisting of a pentamer of ExbB, a dimer of ExbD, and at least one TonB. Electrophysiology studies show that the Ton subcomplex forms pH-sensitive cation-selective channels and provide insight into the mechanism by which it may harness the proton motive force to produce energy.
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http://dx.doi.org/10.1038/nature19757DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5161667PMC
October 2016

Complexity and Dynamics of the Winemaking Bacterial Communities in Berries, Musts, and Wines from Apulian Grape Cultivars through Time and Space.

PLoS One 2016 14;11(6):e0157383. Epub 2016 Jun 14.

Institute of Biomembranes and Bioenergetics, CNR, Bari, Italy.

Currently, there is very little information available regarding the microbiome associated with the wine production chain. Here, we used an amplicon sequencing approach based on high-throughput sequencing (HTS) to obtain a comprehensive assessment of the bacterial community associated with the production of three Apulian red wines, from grape to final product. The relationships among grape variety, the microbial community, and fermentation was investigated. Moreover, the winery microbiota was evaluated compared to the autochthonous species in vineyards that persist until the end of the winemaking process. The analysis highlighted the remarkable dynamics within the microbial communities during fermentation. A common microbial core shared among the examined wine varieties was observed, and the unique taxonomic signature of each wine appellation was revealed. New species belonging to the genus Halomonas were also reported. This study demonstrates the potential of this metagenomic approach, supported by optimized protocols, for identifying the biodiversity of the wine supply chain. The developed experimental pipeline offers new prospects for other research fields in which a comprehensive view of microbial community complexity and dynamics is desirable.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0157383PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907434PMC
July 2017

Difficulties, guidelines and review of developing an acute rejection model after rat intestinal transplantation.

Transpl Immunol 2016 05 19;36:32-41. Epub 2016 Apr 19.

Pediatric Surgery Department, La Paz University Hospital, Paseo La Castellana, 261, 28046 Madrid, Spain. Electronic address:

Experimental small bowel transplantation (SBT) in rats has been proven to be a useful tool for the study of ischemia-reperfusion and immunological aspects related to solid organ transplantation. However, the model is not completely refined, specialized literature is scarce and complex technical details are typically omitted or confusing. Most studies related to acute rejection (AR) use the orthotopic standard, with small sample sizes due to its high mortality, whereas those studying chronic rejection (CR) use the heterotopic standard, which allows longer term survival but does not exactly reflect the human clinical scenario. Various animal strains have been used, and the type of rejection and the timing of its analysis differ among authors. The double purpose of this study was to develop an improved unusual AR model of SBT using the heterotopic technique, and to elaborate a guide useful to implement experimental models for studying AR. We analyzed the model's technical details and expected difficulties in overcoming the learning curve for such a complex microsurgical model, identifying the potential problem areas and providing a step-by-step protocol and reference guide for future surgeons interested in the topic. We also discuss the historic and more recent options in the literature.
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http://dx.doi.org/10.1016/j.trim.2016.04.003DOI Listing
May 2016

Plasma Cholesterol-Lowering Activity of Lard Functionalized with Mushroom Extracts Is Independent of Niemann-Pick C1-like 1 Protein and ABC Sterol Transporter Gene Expression in Hypercholesterolemic Mice.

J Agric Food Chem 2016 Mar 22;64(8):1686-94. Epub 2016 Feb 22.

Department of Experimental Surgery, Research Institute Hospital La Paz (IdiPAZ) , Paseo de la Castellana 261, 28046 Madrid, Spain.

Interest in food matrices supplemented with mushrooms as hypocholesterolemic functional foods is increasing. This study was to (i) investigate the hypocholesterolemic activity of lard functionalized with mushroom extracts (LF) including fungal β-glucans, water-soluble polysaccharides, or ergosterol and (ii) examine the LF influence on transcriptional mechanisms involved in cholesterol metabolism. mRNA levels of 17 cholesterol-related genes were evaluated in jejunum, cecum, and liver of high cholesterol-fed mice. The four tested LFs decreased plasma cholesterol by 22-42%, HDLc by 18-40%, and LDLc by 27-51%, and two of them increased mRNA levels of jejunal Npc1l1 and Abcg5 and hepatic Npc1l1. mRNA levels of other cholesterol-related genes were unchanged. These findings suggest that LF may have potential as a dietary supplement for counteracting diet-induced hypercholesterolemia and could be a source for the development of novel cholesterol-lowering functional foods. However, the cholesterol-lowering effect was unrelated to transcriptional changes, suggesting that post-transcriptional mechanisms could be involved.
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http://dx.doi.org/10.1021/acs.jafc.5b05490DOI Listing
March 2016

Growth Hormone Protects the Intestine Preserving Radiotherapy Efficacy on Tumors: A Short-Term Study.

PLoS One 2015 15;10(12):e0144537. Epub 2015 Dec 15.

Experimental Surgery Department, La Paz Hospital Research Institute, Madrid, Spain.

The efficacy of radiotherapy on tumors is hampered by its devastating adverse effects on healthy tissue, particularly that of the gastrointestinal tract. These effects cause acute symptoms that are so disruptive to patients that they can lead to interruption of the radiotherapy program. These adverse effects could limit the intensity of radiation received by the patient, resulting in a sublethal dose to the tumor, thus increasing the risk of tumor resistance. The lack of an effective treatment to protect the bowel during radiation therapy to allow higher radiation doses that are lethal to the tumor has become a barrier to implementing effective therapy. In this study, we present a comparative analysis of both intestinal and tumor tissue in regard to the efficacy and the preventive impact of a short-term growth hormone (GH) treatment in tumor-bearing rats as a protective agent during radiotherapy. Our data show that the exogenous administration of GH improved intestinal recovery after radiation treatment while preserving the therapeutic effect against the tumor. GH significantly increased proliferation in the irradiated intestine but not in the irradiated tumors, as assessed by Positron Emission Tomography and the proliferative markers Ki67, cyclin D3, and Proliferating Cell Nuclear Antigen. This proliferative effect was consistent with a significant increase in irradiated intestinal villi and crypt length. Furthermore, GH significantly decreased caspase-3 activity in the intestine, whereas GH did not produce this effect in the irradiated tumors. In conclusion, short-term GH treatment protects the bowel, inducing proliferation while reducing apoptosis in healthy intestinal tissue and preserving radiotherapy efficacy on tumors.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0144537PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4682900PMC
June 2016

Modulation of Cholesterol-Related Gene Expression by Dietary Fiber Fractions from Edible Mushrooms.

J Agric Food Chem 2015 Aug 18;63(33):7371-80. Epub 2015 Aug 18.

Department of Production and Characterization of Novel Foods, CIAL - Research Institute in Food Science (UAM+CSIC), Universidad Autónoma de Madrid , C/Nicolas Cabrera 9, Campus de Cantoblanco, 28049 Madrid, Spain.

Mushrooms are a source of dietary fiber (DF) with a cholesterol-lowering effect. However, their underlying mechanisms are poorly understood. The effect of DF-enriched fractions from three mushrooms species on cholesterol-related expression was studied in vitro. The Pleurotus ostreatus DF fraction (PDF) was used in mice models to assess its potential palliative or preventive effect against hypercholesterolemia. PDF induced a transcriptional response in Caco-2 cells, suggesting a possible cholesterol-lowering effect. In the palliative setting, PDF reduced hepatic triglyceride likely because Dgat1 was downregulated. However, cholesterol-related biochemical data showed no changes and no relation with the observed transcriptional modulation. In the preventive setting, PDF modulated cholesterol-related genes expression in a manner similar to that of simvastatin and ezetimibe in the liver, although no changes in plasma and liver biochemical data were induced. Therefore, PDF may be useful reducing hepatic triglyceride accumulation. Because it induced a molecular response similar to hypocholesterolemic drugs in liver, further dose-dependent studies should be carried out.
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http://dx.doi.org/10.1021/acs.jafc.5b02942DOI Listing
August 2015

BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS.

BMC Bioinformatics 2015 Jul 1;16:203. Epub 2015 Jul 1.

Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, via Amendola 165/A, Bari, 70126, Italy.

Background: Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial communities in any environmental niche. If the investigation is aimed only at the microbiome taxonomic structure, a target-based metagenomic approach, here also referred as Meta-barcoding, is generally applied. This approach commonly involves the selective amplification of a species-specific genetic marker (DNA meta-barcode) in the whole taxonomic range of interest and the exploration of its taxon-related variants through High-Throughput Sequencing (HTS) technologies. The accessibility to proper computational systems for the large-scale bioinformatic analysis of HTS data represents, currently, one of the major challenges in advanced Meta-barcoding projects.

Results: BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a new bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the raw sequencing data from either Roche 454 or Illumina HTS platforms, following two alternative paths, respectively. BioMaS is implemented into a public web service available at https://recasgateway.ba.infn.it/ and is also available in Galaxy at http://galaxy.cloud.ba.infn.it:8080 (only for Illumina data).

Conclusion: BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. A comparative benchmark, carried out by using a simulated dataset suitably designed to broadly represent the currently known bacterial and fungal world, showed that BioMaS outperforms QIIME and MOTHUR in terms of extent and accuracy of deep taxonomic sequence assignments.
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http://dx.doi.org/10.1186/s12859-015-0595-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4486701PMC
July 2015

e-DNA meta-barcoding: from NGS raw data to taxonomic profiling.

Methods Mol Biol 2015 ;1269:257-78

Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, 70126, Italy.

In recent years, thanks to the essential support provided by the Next-Generation Sequencing (NGS) technologies, Metagenomics is enabling the direct access to the taxonomic and functional composition of mixed microbial communities living in any environmental niche, without the prerequisite to isolate or culture the single organisms. This approach has already been successfully applied for the analysis of many habitats, such as water or soil natural environments, also characterized by extreme physical and chemical conditions, food supply chains, and animal organisms, including humans. A shotgun sequencing approach can lead to investigate both organisms and genes diversity. Anyway, if the purpose is limited to explore the taxonomic complexity, an amplicon-based approach, based on PCR-targeted sequencing of selected genetic species markers, commonly named "meta-barcodes", is desirable. Among the genomic regions most widely used for the discrimination of bacterial organisms, in some cases up to the species level, some hypervariable domains of the gene coding for the 16S rRNA occupy a prominent place. The amplification of a certain meta-barcode from a microbial community through the use of PCR primers able to work in the entire considered taxonomic group is the first task after the extraction of the total DNA. Generally, this step is followed by the high-throughput sequencing of the resulting amplicons libraries by means of a selected NGS platform. Finally, the interpretation of the huge amount of produced data requires appropriate bioinformatics tools and know-how in addition to efficient computational resources. Here a computational methodology suitable for the taxonomic characterization of 454 meta-barcode sequences is described in detail. In particular, a dataset covering the V1-V3 region belonging to the bacterial 16S rRNA coding gene and produced in the Human Microbiome Project (HMP) from a palatine tonsils sample is analyzed. The proposed exercise includes the basic steps to manage raw sequencing data, remove amplification and pyrosequencing errors, and finally map sequences on the taxonomy.
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http://dx.doi.org/10.1007/978-1-4939-2291-8_16DOI Listing
September 2015

Nuclear α1-antichymotrypsin promotes chromatin condensation and inhibits proliferation of human hepatocellular carcinoma cells.

Gastroenterology 2013 Apr 4;144(4):818-828.e4. Epub 2013 Jan 4.

Division of Hepatology and Gene Therapy, Centro de Investigación Médica Aplicada (CIMA), University of Navarra, Pamplona, Spain.

Background & Aims: α1-Antichymotrypsin (α1-ACT), a member of the serpin family (SERPINA3), is an acute-phase protein secreted by hepatocytes in response to cytokines such as oncostatin M. α1-ACT is a protease inhibitor thought to limit tissue damage produced by excessive inflammation-associated proteolysis. However, α1-ACT also is detected in the nuclei of cells, where its activities are unknown. Expression of α1-ACT is down-regulated in human hepatocellular carcinoma (HCC) tissues and cells; we examined its roles in liver regeneration and HCC proliferation.

Methods: We measured levels of α1-ACT messenger RNA in human HCC samples and healthy liver tissue. We reduced levels of α1-ACT using targeted RNA interference in human HCC (HepG2) and mouse hepatocyte (AML12) cell lines, and overexpressed α1-ACT from lentiviral vectors in Huh7 (HCC) cells and adeno-associated viral vectors in livers of mice. We assessed proliferation, differentiation, and chromatin compaction in cultured cells, and liver regeneration and tumor formation in mice.

Results: Reducing levels of α1-ACT promoted proliferation of HCC cells in vitro. Oncostatin M up-regulated α1-ACT expression and nuclear translocation, which inhibited HCC cell proliferation and activated differentiation of mouse hepatocytes. We identified amino acids required for α1-ACT nuclear localization, and found that α1-ACT inhibits cell-cycle progression and anchorage-independent proliferation of HCC cells. HCC cells that overexpressed α1-ACT formed smaller tumors in mice than HCC cells that did not express the protein. α1-ACT was observed to self-associate and polymerize in the nuclei of cells; nuclear α1-ACT strongly bound chromatin to promote a condensed state that could prevent cell proliferation.

Conclusions: α1-ACT localizes to the nuclei of hepatic cells to control chromatin condensation and proliferation. Overexpression of α1-ACT slows the growth of HCC xenograft tumors in nude mice.
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http://dx.doi.org/10.1053/j.gastro.2012.12.029DOI Listing
April 2013

Regulation of amphiregulin gene expression by β-catenin signaling in human hepatocellular carcinoma cells: a novel crosstalk between FGF19 and the EGFR system.

PLoS One 2012 20;7(12):e52711. Epub 2012 Dec 20.

Division of Hepatology and Gene Therapy, Centre for Applied Medical Research, University of Navarra, Pamplona, Spain.

Hepatocellular carcinoma (HCC) is the most prevalent liver tumor and a deadly disease with limited therapeutic options. Dysregulation of cell signaling pathways is a common denominator in tumorigenesis, including hepatocarcinogenesis. The epidermal growth factor receptor (EGFR) signaling system is commonly activated in HCC, and is currently being evaluated as a therapeutic target in combination therapies. We and others have identified a central role for the EGFR ligand amphiregulin (AR) in the proliferation, survival and drug resistance of HCC cells. AR expression is frequently up-regulated in HCC tissues and cells through mechanisms not completely known. Here we identify the β-catenin signaling pathway as a novel mechanism leading to transcriptional activation of the AR gene in human HCC cells. Activation of β-catenin signaling, or expression of the T41A β-catenin active mutant, led to the induction of AR expression involving three specific β-catenin-Tcf responsive elements in its proximal promoter. We demonstrate that HCC cells expressing the T41A β-catenin active mutant show enhanced proliferation that is dependent in part on AR expression and EGFR signaling. We also demonstrate here a novel cross-talk of the EGFR system with fibroblast growth factor 19 (FGF19). FGF19 is a recently identified driver gene in hepatocarcinogenesis and an activator of β-catenin signaling in HCC and colon cancer cells. We show that FGF19 induced AR gene expression through the β-catenin pathway in human HCC cells. Importantly, AR up-regulation and EGFR signaling participated in the induction of cyclin D1 and cell proliferation elicited by FGF19. Finally, we demonstrate a positive correlation between FGF19 and AR expression in human HCC tissues, therefore supporting in clinical samples our experimental observations. These findings identify the AR/EGFR system as a key mediator of FGF19 responses in HCC cells involving β-catenin signaling, and suggest that combined targeting of FGF19 and AR/EGFR may enhance therapeutic efficacy.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0052711PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3527604PMC
June 2013

Reference databases for taxonomic assignment in metagenomics.

Brief Bioinform 2012 Nov 10;13(6):682-95. Epub 2012 Jul 10.

Institute of Biomembranes and Bioenergetics, National Research Council, Bari, Italy.

Metagenomics is providing an unprecedented access to the environmental microbial diversity. The amplicon-based metagenomics approach involves the PCR-targeted sequencing of a genetic locus fitting different features. Namely, it must be ubiquitous in the taxonomic range of interest, variable enough to discriminate between different species but flanked by highly conserved sequences, and of suitable size to be sequenced through next-generation platforms. The internal transcribed spacers 1 and 2 (ITS1 and ITS2) of the ribosomal DNA operon and one or more hyper-variable regions of 16S ribosomal RNA gene are typically used to identify fungal and bacterial species, respectively. In this context, reliable reference databases and taxonomies are crucial to assign amplicon sequence reads to the correct phylogenetic ranks. Several resources provide consistent phylogenetic classification of publicly available 16S ribosomal DNA sequences, whereas the state of ribosomal internal transcribed spacers reference databases is notably less advanced. In this review, we aim to give an overview of existing reference resources for both types of markers, highlighting strengths and possible shortcomings of their use for metagenomics purposes. Moreover, we present a new database, ITSoneDB, of well annotated and phylogenetically classified ITS1 sequences to be used as a reference collection in metagenomic studies of environmental fungal communities. ITSoneDB is available for download and browsing at http://itsonedb.ba.itb.cnr.it/.
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http://dx.doi.org/10.1093/bib/bbs036DOI Listing
November 2012

Dynamic response of thin-film semiconductors to AC voltage perturbations.

Chemphyschem 2012 Aug 8;13(12):2910-8. Epub 2012 May 8.

Zentrum für Elektrochemie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany.

A theoretical treatment of a Schottky barrier dynamic response is developed on the basis of a general model of a semiconductor with thickness comparable in length to the space charge region width. It is shown that, when the space charge region approaches the metal/semiconductor interface, the electric field at this interface, induced by the charge accumulated on the metal, becomes significant with respect to the electric field induced by the charge accumulated on the semiconductor. Under this condition, the total capacitance of the Schottky barrier becomes independent of the polarization potential and tends to the value ε/L, like in a pure dielectric insulator. The term thin film is intended to be with respect to the screening length, which is a function of the volumetric charge density. In amorphous materials the transition potential at which the semiconducting to insulating behaviour is observed is dependent on the frequency. An approximated analytical solution for the capacitance of the junction is calculated. The model for finite thickness semiconductors is successfully applied to the study of anodic Nb(2)O(5), formed in phosphate buffer 0.5 M aqueous solution up to different formation potentials (namely 5, 10 and 20 V vs. Ag/AgCl). The finite thickness semiconductor model permits extrapolation to a general behaviour of the oxide in a wide range of frequencies, potentials and thicknesses, and identification of the electron transfer between adsorbed surface species and the conduction band of Nb(2)O(5) at potentials near to the flat band value.
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http://dx.doi.org/10.1002/cphc.201200226DOI Listing
August 2012

Searching for a needle in the haystack: comparing six methods to evaluate heteroplasmy in difficult sequence context.

Biotechnol Adv 2012 Jan-Feb;30(1):363-71. Epub 2011 Jun 13.

Ostetriche e Pediatriche, Genetica Medica, Pol. Universitario S.Orsola-Malpighi, Bologna, Italy.

Mitochondrial DNA (mtDNA) mutations have been involved in disease, aging and cancer and furthermore exploited for evolutionary and forensic investigation. When investigating mtDNA mutations the peculiar aspects of mitochondrial genetics, such as heteroplasmy and threshold effect, require suitable approaches which must be sensitive enough to detect low-level heteroplasmy and, precise enough to quantify the exact mutational load. In order to establish the optimal approach for the evaluation of heteroplasmy, six methods were experimentally compared for their capacity to reveal and quantify mtDNA variants. Drawbacks and advantages of cloning, Fluorescent PCR (F-PCR), denaturing High Performance Liquid Chromatography (dHPLC), quantitative Real-Time PCR (qRTPCR), High Resolution Melting (HRM) and 454 pyrosequencing were determined. In particular, detection and quantification of a mutation in a difficult sequence context were investigated, through analysis of an insertion in a homopolymeric stretch (m.3571insC).
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http://dx.doi.org/10.1016/j.biotechadv.2011.06.001DOI Listing
July 2012

The epidermal growth factor receptor ligand amphiregulin is a negative regulator of hepatic acute-phase gene expression.

J Hepatol 2009 Dec 12;51(6):1010-20. Epub 2009 Sep 12.

Division of Hepatology and Gene Therapy, CIMA, University of Navarra, Avda. Pio XII n. 55, 31008 Pamplona, Spain.

Background/aims: The modulation of the hepatic acute-phase reaction (APR) that occurs during inflammation and liver regeneration is important for allowing normal hepatocellular proliferation and the restoration of homeostasis. Activation of acute-phase protein (APP) gene expression by interleukin-6 (IL-6)-type cytokines is thought to be counteracted by growth factors released during hepatic inflammation and regeneration. The epidermal growth factor receptor (EGFR) ligand amphiregulin (AR) is readily induced by inflammatory signals and plays a nonredundant protective role during liver injury. In this paper, we investigated the role of AR as a modulator of liver APP gene expression.

Methods: Expression of APP genes was measured in the livers of AR(+/+) and AR(-/-)mice during inflammation and regeneration and in cultured liver cells treated with AR and oncostatin M (OSM). Crosstalk between AR and OSM signalling was studied.

Results: APP genes were overexpressed in the livers of AR(-/-) mice during inflammation and hepatocellular regeneration. In cultured AR-null hepatocytes and human hepatocellular carcinoma (HCC) cells after AR knockdown, APP gene expression is enhanced. AR counteracts OSM-triggered signal transducer and activator of transcription 3 signalling in hepatocytes and attenuates APP gene transcription.

Conclusions: Our data support the relevance of EGFR-mediated signalling in the modulation of cytokine-activated pathways. We have identified AR as a key regulator of hepatic APP gene expression during inflammation and liver regeneration.
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http://dx.doi.org/10.1016/j.jhep.2009.06.030DOI Listing
December 2009

Towards barcode markers in Fungi: an intron map of Ascomycota mitochondria.

BMC Bioinformatics 2009 Jun 16;10 Suppl 6:S15. Epub 2009 Jun 16.

CNR - Istituto di Tecnologie Biomediche, Sede di Bari, Via Amendola 122/D, Bari, 70126, Italy.

Background: A standardized and cost-effective molecular identification system is now an urgent need for Fungi owing to their wide involvement in human life quality. In particular the potential use of mitochondrial DNA species markers has been taken in account. Unfortunately, a serious difficulty in the PCR and bioinformatic surveys is due to the presence of mobile introns in almost all the fungal mitochondrial genes. The aim of this work is to verify the incidence of this phenomenon in Ascomycota, testing, at the same time, a new bioinformatic tool for extracting and managing sequence databases annotations, in order to identify the mitochondrial gene regions where introns are missing so as to propose them as species markers.

Methods: The general trend towards a large occurrence of introns in the mitochondrial genome of Fungi has been confirmed in Ascomycota by an extensive bioinformatic analysis, performed on all the entries concerning 11 mitochondrial protein coding genes and 2 mitochondrial rRNA (ribosomal RNA) specifying genes, belonging to this phylum, available in public nucleotide sequence databases. A new query approach has been developed to retrieve effectively introns information included in these entries.

Results: After comparing the new query-based approach with a blast-based procedure, with the aim of designing a faithful Ascomycota mitochondrial intron map, the first method appeared clearly the most accurate. Within this map, despite the large pervasiveness of introns, it is possible to distinguish specific regions comprised in several genes, including the full NADH dehydrogenase subunit 6 (ND6) gene, which could be considered as barcode candidates for Ascomycota due to their paucity of introns and to their length, above 400 bp, comparable to the lower end size of the length range of barcodes successfully used in animals.

Conclusion: The development of the new query system described here would answer the pressing requirement to improve drastically the bioinformatics support to the DNA Barcode Initiative. The large scale investigation of Ascomycota mitochondrial introns performed through this tool, allowing to exclude the introns-rich sequences from the barcode candidates exploration, could be the first step towards a mitochondrial barcoding strategy for these organisms, similar to the standard approach employed in metazoans.
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http://dx.doi.org/10.1186/1471-2105-10-S6-S15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2697638PMC
June 2009

The epidermal growth factor receptor: a link between inflammation and liver cancer.

Exp Biol Med (Maywood) 2009 Jul 8;234(7):713-25. Epub 2009 May 8.

Division of Hepatology and Gene Therapy, CIMA-Universidad de Navarra, 31008 Pamplona, Spain.

Epidemiological studies have established that many tumours occur in association with persistent inflammation. One clear example of inflammation-related cancer is hepatocellular carcinoma (HCC). HCC slowly unfolds on a background of chronic inflammation triggered by exposure to infectious agents (hepatotropic viruses), toxic compounds (ethanol), or metabolic impairment. The molecular links that connect inflammation and cancer are not completely known, but evidence gathered over the past few years is beginning to define the precise mechanisms. A central role for cytokines such as interleukin-6 (IL-6) and IL-1 (alpha and beta) in liver cancer has been established in experimental models. Besides these inflammatory mediators, mounting evidence points to the dysregulation of specific growth and survival-related pathways in HCC development. Among them is the pathway governed by the epidermal growth factor receptor (EGFR), which can be bound and activated by a broad family of ligands. Of special relevance is the fact that the EGFR engages in extensive crosstalk with other signaling pathways, serving as a "signaling hub" for an increasing list of growth factors, cytokines, and inflammatory mediators. In this review, we summarize the most recent evidences supporting a role for the EGFR system in inflammation-related cell signaling, with special emphasis in liver inflammation and HCC. The molecular dissection of the pathways connecting the inflammatory reaction and neoplasia will facilitate the development of novel and more effective antitumor strategies.
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http://dx.doi.org/10.3181/0901-MR-12DOI Listing
July 2009
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