Papers by Raffaele Calogero
Methods in molecular medicine
The use of recombinant antigens is essential for the construction of robust and sensitive diagnos... more The use of recombinant antigens is essential for the construction of robust and sensitive diagnostic assays. A critical step in the preparation of recombinant antigens is protein purification. Purification problems may be very different for related structural proteins expressed in the same host or for the same protein expressed in different hosts, because the biochemical characteristics of a recombinant protein, expressed in a heterologous system, are unique. In this chapter we make a brief introduction to protein purification procedures and we present a quick purification process suitable for the isolation of recombinant protein having high isoelectric points encoding non-conformational epitopes.
Molecular Cell, 2015
The Hippo/YAP signaling pathway is a crucial regulator of tissue growth, stem cell activity, and ... more The Hippo/YAP signaling pathway is a crucial regulator of tissue growth, stem cell activity, and tumorigenesis. However, the mechanism by which YAP controls transcription remains to be fully elucidated. Here, we utilize global chromatin occupancy analyses to demonstrate that robust YAP binding is restricted to a relatively small number of distal regulatory elements in the genome. YAP occupancy defines a subset of enhancers and superenhancers with the highest transcriptional outputs. YAP modulates transcription from these elements predominantly by regulating promoter-proximal polymerase II (Pol II) pause release. Mechanistically, YAP interacts and recruits the Mediator complex to enhancers, allowing the recruitment of the CDK9 elongating kinase. Genetic and chemical perturbation experiments demonstrate the requirement for Mediator and CDK9 in YAP-driven phenotypes of overgrowth and tumorigenesis. Our results here uncover the molecular mechanisms employed by YAP to exert its growth and oncogenic functions, and suggest strategies for intervention.
Journal of Nutrition, 2007
Conjugated linoleic acid (CLA) exhibits isomer-specific effects on transepithelial calcium (Ca) t... more Conjugated linoleic acid (CLA) exhibits isomer-specific effects on transepithelial calcium (Ca) transport as well as on cell growth in human intestinal-like Caco-2 cells. However, the molecular mechanisms of action are still unclear. Therefore, this study used a transcriptomic approach to help elucidate the molecular mechanisms underlying such isomer-specific effects. Caco-2 cells were treated with 80 µmol/L linoleic acid (control), 80
STRIRED is a toolkit to generate a graphical picture of the distribution of 4-to 6-mer repeats in... more STRIRED is a toolkit to generate a graphical picture of the distribution of 4-to 6-mer repeats in a set of user-defined nucleic acid sequences. Availability: The STRIRED package can be downloaded as self-extracting archive (strired.exe) by anonymous FTP from biol.dgbm.unina.it (143.225.252.1), in the directory /software/ win95/STRIRED.
Bioinformatics
VIRTLAB is a self-training program based on PBL (Problem-Based-Learning Pathway) built to simulat... more VIRTLAB is a self-training program based on PBL (Problem-Based-Learning Pathway) built to simulate a molecular biology laboratory It has been designed to stimulate students in the biological sciences to analyse and solve molecular biology problems using standard laboratory techniques (e.g. restriction enzyme digestions, analytical and preparative agarose gels, DNA cloning and sequencing, etc.) and can thus be viewed as a teaching aid.
Methods in molecular medicine
DNA microarray is an innovative technology for obtaining information on gene function. Because it... more DNA microarray is an innovative technology for obtaining information on gene function. Because it is a high-throughput method, computational tools are essential in data analysis and mining to extract the knowledge from experimental results. Filtering procedures and statistical approaches are frequently combined to identify differentially expressed genes. However, obtaining a list of differentially expressed genes is only the starting point because an important step is the integration of differential expression profiles in a biological context, which is a hot topic in data mining. In this chapter an integrated approach of filtering and statistical validation to select trustable differentially expressed genes is described together with a brief introduction on data mining focusing on the classification of co-regulated genes on the basis of their biological function.
American Journal of Cancer Research
Vaccines are one of the main arms of preventive medicine. Recently a large series of experiments ... more Vaccines are one of the main arms of preventive medicine. Recently a large series of experiments with cancer-prone genetically engineered mice have shown that preventive vaccines are also extremely efficacious inhibitors of the progression of carcinogenesis. Early vaccination affords significant and persistent protection, whereas its efficacy fades when neoplastic lesions become more advanced. Our current attempts to use combination strategies and technological advances to make vaccines effective in cancer prevention able to cure more advanced stages of cancer lesions are based on the temporary and systemic T(reg) removal, the preparation of new bimodular plasmids for DNA vaccination, and the search for fresh target oncoantigens.
European Journal of Cancer Supplements, 2008
polyclonal activation and transduction with retroviral vectors. In vivo experiments are in progre... more polyclonal activation and transduction with retroviral vectors. In vivo experiments are in progress to determine whether in vivo survival of transduced T cells can be influenced by the in vitro transduction method.
BMC Systems Biology, 2015
Nowadays multidisciplinary approaches combining mathematical models with experimental assays are ... more Nowadays multidisciplinary approaches combining mathematical models with experimental assays are becoming relevant for the study of biological systems. Indeed, in cancer research multidisciplinary approaches are successfully used to understand the crucial aspects implicated in tumor growth. In particular, the Cancer Stem Cell (CSC) biology represents an area particularly suited to be studied through multidisciplinary approaches, and modeling has significantly contributed to pinpoint the crucial aspects implicated in this theory. The study of a new model on the CSC-based tumor progression has been the motivation to design a new work-flow that helps to characterize possible system dynamics and to identify those parameters influencing such behaviors. In detail, we extended our recent model on CSC-dynamics creating a new system capable of describing tumor growth during the different stages of cancer progression. Indeed, tumor cells appear to progress through lineage stages like those of normal tissues, being their division auto-regulated by internal feedback mechanisms. These new features have introduced some non-linearities in the model, making it more difficult to be studied by solely analytical techniques. Our new work-flow, based on statistical methods, was used to identify the parameters which influence the tumor growth. The effectiveness of the presented work-flow was firstly verified on two well known models and then applied to investigate our extended CSC model. We propose a new work-flow to study in a practical and informative way complex systems, allowing an easy identification, interpretation, and visualization of the key model parameters. Our methodology is useful to investigate possible model behaviors and to establish factors driving model dynamics.
American journal of physiology. Heart and circulatory physiology, 2014
Cardiac overexpression of locally acting muscle-restricted (m)IGF-1 and the consequent downstream... more Cardiac overexpression of locally acting muscle-restricted (m)IGF-1 and the consequent downstream activation of NAD(+)-dependent protein deacetylase sirtuin 1 (SIRT1) trigger potent cardiac antioxidative and antihypertrophic effects. Transient receptor potential (TRP) cation channel A1 (TRPA1) belongs to the TRP ion channel family of molecular detectors of thermal and chemical stimuli that activate sensory neurons to produce pain. Recently, it has been shown that TRPA1 activity influences blood pressure, but the significance of TRPA1 in the cardiovascular system remains elusive. In the present work, using genomic screening in mouse hearts, we found that TRPA1 is a target of mIGF-1/SIRT1 signaling. TRPA1 expression is increased in the heart of cardiac-restricted mIGF-1 transgenic (Tg) mice, both in cardiomyocytes and noncardiomyocytes. In wild-type mice, SIRT1 occupied the TRPA1 promoter, inhibiting its expression, whereas in the presence of the cardiac mIGF-1 transgene, SIRT1 was di...
Biochemical Education, 1996
Comparative and functional genomics, 2003
DNA microarray technology is a high-throughput method for gaining information on gene function. M... more DNA microarray technology is a high-throughput method for gaining information on gene function. Microarray technology is based on deposition/synthesis, in an ordered manner, on a solid surface, of thousands of EST sequences/genes/oligonucleotides. Due to the high number of generated datapoints, computational tools are essential in microarray data analysis and mining to grasp knowledge from experimental results. In this review, we will focus on some of the methodologies actually available to define gene expression intensity measures, microarray data normalization, and statistical validation of differential expression.
BioMed research international, 2013
Aging, 2012
Locally acting insulin growth factor isoform (mIGF-1) and the NAD+-dependent protein deacetylase ... more Locally acting insulin growth factor isoform (mIGF-1) and the NAD+-dependent protein deacetylase SIRT1 are implicated in life and health span. Heart failure is associated with aging and is a major cause of death. mIGF-1 protects the heart from oxidative stresses via SIRT1. SIRT1 subcellular localization and its genomic regulation by mIGF-1 are unknown. We show here that SIRT1 is located in the nuclei of a significant fraction of cardiomyocytes. Using high throughput sequencing approaches in mIGF-1 transgenic mice, we identified new targets of the mIGF-1/SIRT1 signaling. In addition to its potent cardioprotective properties, cardiac-restricted mIGF-1 transgene induced systemic changes such as high blood pressure, leukocytosis and an enhanced fear response, in a SIRT1-dependent manner. Cardiac mIGF-1/ SIRT1 signaling may thus modulate disparate systemic functions.
Briefings in functional genomics & proteomics, 2007
Microarray based transcription profiling is now a consolidated methodology and has widespread use... more Microarray based transcription profiling is now a consolidated methodology and has widespread use in areas such as pharmacogenomics, diagnostics and drug target identification. Large-scale microarray studies are also becoming crucial to a new way of conceiving experimental biology. A main issue in microarray transcription profiling is data analysis and mining. When microarrays became a methodology of general use, considerable effort was made to produce algorithms and methods for the identification of differentially expressed genes. More recently, the focus has switched to algorithms and database development for microarray data mining. Furthermore, the evolution of microarray technology is allowing researchers to grasp the regulative nature of transcription, integrating basic expression analysis with mRNA characteristics, i.e. exon-based arrays, and with DNA characteristics, i.e. comparative genomic hybridization, single nucleotide polymorphism, tiling and promoter structure. In this...
The Journal of nutrition, 2007
Conjugated linoleic acid (CLA) exhibits isomer-specific effects on transepithelial calcium (Ca) t... more Conjugated linoleic acid (CLA) exhibits isomer-specific effects on transepithelial calcium (Ca) transport as well as on cell growth in human intestinal-like Caco-2 cells. However, the molecular mechanisms of action are still unclear. Therefore, this study used a transcriptomic approach to help elucidate the molecular mechanisms underlying such isomer-specific effects. Caco-2 cells were treated with 80 micromol/L linoleic acid (control), 80 micromol/L trans-10, cis-12 CLA, or 80 micromol/L cis-9, trans-11 CLA for 12 d. Ca transport was measured radio-isotopically. RNA was isolated from the cells, labeled, and hybridized to the Affymetrix U133 2.0 Plus arrays (n = 3). Data and functional analysis was preformed using Bioconductor. Using a minimum fold-change criterion of 1.6 and a false discovery rate criterion of P-value <or= 0.05, trans-10, cis-12 CLA altered the expression of 918 genes, whereas, cis-9, trans-11 CLA had no effect on gene expression. Gene ontology analysis revealed...
Methods in molecular medicine, 2004
DNA microarray is an innovative technology for obtaining information on gene function. Because it... more DNA microarray is an innovative technology for obtaining information on gene function. Because it is a high-throughput method, computational tools are essential in data analysis and mining to extract the knowledge from experimental results. Filtering procedures and statistical approaches are frequently combined to identify differentially expressed genes. However, obtaining a list of differentially expressed genes is only the starting point because an important step is the integration of differential expression profiles in a biological context, which is a hot topic in data mining. In this chapter an integrated approach of filtering and statistical validation to select trustable differentially expressed genes is described together with a brief introduction on data mining focusing on the classification of co-regulated genes on the basis of their biological function.
The Journal of biological chemistry, Jan 27, 2001
The INK4a gene, one of the most often disrupted loci in human cancer, encodes two unrelated prote... more The INK4a gene, one of the most often disrupted loci in human cancer, encodes two unrelated proteins, p16(INK4a) and p14(ARF) (ARF) both capable of inducing cell cycle arrest. Although it has been clearly demonstrated that ARF inhibits cell cycle via p53 stabilization, very little is known about the involvement of ARF in other cell cycle regulatory pathways, as well as on the mechanisms responsible for activating ARF following oncoproliferative stimuli. In search of factors that might associate with ARF to control its activity or its specificity, we performed a yeast two-hybrid screen. We report here that the human homologue of spinophilin/neurabin II, a regulatory subunit of protein phosphatase 1 catalytic subunit specifically interacts with ARF, both in yeast and in mammalian cells. We also show that ectopic expression of spinophilin/neurabin II inhibits the formation of G418-resistant colonies when transfected into human and mouse cell lines, regardless of p53 and ARF status. Mor...
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Papers by Raffaele Calogero