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The original version of this Letter contains an error in Figure 5, concerning an experiment performed at University of Bologna, which shows the effect of the tested compounds on microglial activation. In the incorrect published Figure 5, the GAPDH band (housekeeping protein used as loading control) from a preliminary experiment for compound 1 was accidentally shown, and the correct image is used below. Furthermore, since we used the same LPS-treated control microglial cells for compounds 11 and 12, being that they were tested in the same experiment and plate, the right two panels have been modified for clarity. This is the correct Figure 5:.(Figure Presented).

Environmental temperature variations affect many properties and functions of biomolecules and structural components at the cellular level, and influence the animal physiology and behavior at the organism level. It is well accepted that the biochemical changes induced by temperature stress are attributed to gene expression modulations. The aim of this work was to understand the molecular mechanism and the behavioural responses correlated to temperature stress in zebrafish (Danio rerio), which is a widely used animal model for environmental genomics researches. Adult specimens of wild type zebrafish were kept at three different temperatures: 18°C, 34°C and 26°C (used as a control) for 21 days and then subjected to behavioural tests using a YMaze task to evaluate the response to novelty and the spatial memory. Proteomic analysis were carried out on brains to evaluate the thermal effect at the central nervous system level. Briefly, for each temperature 9 brains were lysed and after reduction and derivatization, the proteins were digested with trypsin. LC-ESI MS/MS analysis was performed on a Dionex UltiMate 3000 HPLC. The eluate was electrosprayed into an LTQ Orbitrap Velos. Four technical replicate analyses of each sample were performed. Mass spectra were analyzed using MaxQuant and Peak Studio software. Finally, the bioinformatic analysis was carried out by DAVID and PANTHER softwares to evaluate enriched categories filtered for biological processes, molecular function (MF), cellular component (CC) and pathways involved. Preliminary results suggest that thermal stress at the cellular level influences the CC organization, biogenesis, structural morphogenesis and MF and at the organism level affects the interest for the new environment and the spatial memory.

Introduction. Mastocytosis is a myeloid neoplasm characterized by abnormal accumulation and frequent activation of mast cells (MCs) in various organs. The recent WHO classification (2008) includes an indolent form (ISM), an aggressive form (ASM) and a leukemic subvariant (MCL). The c-kit mutation D816V is detectable in most adult patients with SM. Treatment of SM usually focuses on symptom relief by histamine receptor antagonists and other supportive therapy. However, in aggressive and leukemic variants, cytoreductive and targeted drugs must be applied. Methods. From 2008, 22 patients (male/female=11/11) affected by SM have been referred to our Institution. Among these, 12 (55%) presented with systemic symptoms associated with signs of organ involvement (skeletal lesions, ascites, liver function impairment or bon marrow disfunction), thus identifying an ASM. Therefore, since a first line therapy (IFNalfa, Imatinib and 2CdA in 56%, 11% and 33% of the patients, respectively) and supportive care with histamine receptor antagonists weren’t followed by a significant benefit, a personalized use of PKC412 was asked and obtained for 9 out of 12 ASM patients. Thus, from March 2011 9 (M/F =3/9) patients with ASM have been treated with PKC412, administered orally, at the dosage of 100 mg twice daily, without rest periods. The median age was 60 years (range 39-75); the median time from diagnosis was 6 months (range 2-53). Median serum tryptase level was 100 mcg/L(range 19.3-1160). C-kit mutation D816V was present in 8 out of 9 patients. Cytogenetic analysis was normal in all the patients. Results. Seven out of nine patients were evaluable for response. The median duration of therapy was 517 days (range 327-970+). According to European Criteria, a Major response was observed in one patient, and a partial response in 6 patients. Overall, the drug was well tolerated, and no serious adverse events were observed. All the patients obtained a quick and prolonged improvement of clinical symptoms, in terms of weight gain, bowel function and skeletal pain. At the bone marrow evaluation, the persistence of the D816V c-kit mutation was observed, despite a significant decrease of mast cell marrow involvement. Conclusions. In a small cohort of ASM patient, the prolonged therapy with PKC412 is safe and effective, mainly on symptoms improvement and haematological profile. Nevertheless, the persistence of the D816V c-kit mutation, despite significant responses, suggests that many other oncogenic factors may be responsible for the pathogenesis of the disease. UDS approaches are needed in order to clarify this issue. Acknowledgments. Work supported by European LeukemiaNet, AIRC, AIL, PRIN 2010-2011, University of Bologna, FP7 NGS-PTL project. Introduction. Mastocytosis is a myeloid neoplasm characterized by abnormal accumulation and frequent activation of mast cells (MCs) in various organs. The recent WHO classification (2008) includes an indolent form (ISM), an aggressive form (ASM) and a leukemic subvariant (MCL). The c-kit mutation D816V is detectable in most adult patients with SM. Treatment of SM usually focuses on symptom relief by histamine receptor antagonists and other supportive therapy. However, in aggressive and leukemic variants, cytoreductive and targeted drugs must be applied. Methods. From 2008, 22 patients (male/female=11/11) affected by SM have been referred to our Institution. Among these, 12 (55%) presented with systemic symptoms associated with signs of organ involvement (skeletal lesions, ascites, liver function impairment or bon marrow disfunction), thus identifying an ASM. Therefore, since a first line therapy (IFNalfa, Imatinib and 2CdA in 56%, 11% and 33% of the patients, respectively) and supportive care with histamine receptor antagonists weren’t followed by a significant benefit, a personalized use of PKC412 was asked and obtained for 9 out of 12 ASM patients. Thus, from March 2011 9 (M/F =3/9) patients with ASM have been treated with PKC412, administered orally, at the dosage of 100 mg twice daily, without rest periods. The median age was 60 years (range 39-75); the median time from diagnosis was 6 months (range 2-53). Median serum tryptase level was 100 mcg/L(range 19.3-1160). C-kit mutation D816V was present in 8 out of 9 patients. Cytogenetic analysis was normal in all the patients. Results. Seven out of nine patients were evaluable for response. The median duration of therapy was 517 days (range 327-970+). According to European Criteria, a Major response was observed in one patient, and a partial response in 6 patients. Overall, the drug was well tolerated, and no serious adverse events were observed. All the patients obtained a quick and prolonged improvement of clinical symptoms, in terms of weight gain, bowel function and skeletal pain. At the bone marrow evaluation, the persistence of the D816V c-kit mutation was observed, despite a significant decrease of mast cell marrow involvement. Conclusions. In a small cohort of ASM patient, the prolonged therapy with PKC412 is safe and effective, mainly on symptoms improvement and haematological profile. Nevertheless, the persistence of the D816V c-kit mutation, despite significant responses, suggests that many other oncogenic factors may be responsible for the pathogenesis of the disease. UDS approaches are needed in order to clarify this issue. Acknowledgments. Work supported by European LeukemiaNet, AIRC, AIL, PRIN 2010-2011, University of Bologna, FP7 NGS-PTL project.

Human rhabdomyosarcoma cells express membrane epidermal growth factor receptor (ECF-R), which could confer responsiveness to EGF and transforming growth factor-alpha (TGF-alpha) of autocrine or paracrine origin. To study the role played by this growth factor circuit in the proliferation and differentiation of myogenic neoplastic cells, human rhabdomyosarcoma EGF-R-expressing cells (RD/18 clone) have been transfected with a plasmid containing a fragment of the EGF-R cDNA in the antisense orientation. In vitro growth and differentiative ability were studied on six antisense-transfected clones (AS) in comparison to parental RD/18 cells and to cells transfected with the plasmid containing only the neomycin resistance gene (NEO). A reduced EGF-R membrane expression was found in AS clones by decreased immunofluorescence with an anti-EGF-R monoclonal antibody. All AS transfectants had a greatly impaired proliferative ability, even when cultured in fetal bovine serum-containing medium. Proliferation of AS clones was completely blocked in medium supplemented with 2% horse serum. The differentiation ability of AS clones was heterogeneous, ranging from clones with a percentage of myosin-positive cells higher than controls to clones with a negligible myosin expression. Therefore, the growth impairment determined by the loop interruption is not sufficient to switch on the differentiation program. The role played by EGF-R in the proliferation of human rhabdomyosarcoma cells suggests that this receptor could constitute a target for a therapeutic approach.

CD40, a membrane glycoprotein of the tumor necrosis factor receptor family, is expressed by several tumor types, including B-cell lymphomas, carcinomas, and melanoma, but little is known concerning its expression by sarcoma. We used flow cytometry to analyze the expression of CD40 in human cell lines derived from 12 osteosarcomas, 6 Ewing's sarcomas, and 5 rhabdomyosarcomas. Detectable CD40 levels ranging from low to very high were found in one-third of osteosarcomas, whereas five of six Ewing's sarcomas expressed intermediate levels of CD40; all rhabdomyosarcomas were CD40-negative. At the tissue level, two of eight primary high-grade osteosarcomas showed CD40-positive immunostaining. Osteosarcoma cells and Ewing's sarcoma cells expressing CD40 were treated with recombinant soluble CD40 ligand to analyze CD40 function. Treatment with soluble CD40 ligand increased the level of apoptotic cells and stimulated the transcription of matrix metalloproteinase 9 gene, enhancing matrix metalloproteinase 9 enzyme secretion. The results indicate that in human osteosarcoma and Ewing's sarcoma, CD40 is a functional receptor whose engagement can have opposite effects on tumor cell survival and malignancy.

Carcinoembryonic antigen (CEA) is a highly glycosylated cell surface glycoprotein belonging to the immunoglobulin superfamily. CEA has been involved in vitro in adhesion mechanisms, but little is known about the function of this glycoprotein in vivo in normal tissue differentiation and malignancy. With regard to the relationship between CEA expression and tissue differentiation, it has been reported that transfection of the CEA gene in rat L6 myoblasts results in a complete block of myogenic differentiation. To extend investigations to the transformed myogenic counterpart and examine CEA effects on differentiation and malignancy outside the colon system, we have transfected the human CEA gene in human rhabdomyosarcoma cells. Human rhabdomyosarcoma cells transfected with the CEA gene correctly expressed membrane CEA anchored via glycosylphosphatidylinositol and secreted CEA in the medium. CEA gene transfer in human rhabdomyosarcoma cells, which display a limited differentiation ability, does not further inhibit myogenic differentiation or alter in vitro proliferation or natural killer sensitivity. CEA transfection does not affect s.c. growth in nude mice, but the ectopic expression of CEA in human rhabdomyosarcoma cells can strongly inhibit their metastatic ability to lungs and adrenals after i.v. injection. The impairment of metastatic potential correlates with a reduction in the homotypic adhesion properties of the cells. These data suggest that CEA, in some systems, can interfere with intercellular adhesion and, at least for cells not metastatic to the liver, can act as an anti-metastatic molecule.

[Image: see text] Several evidence pointed out the role of epigenetics in Alzheimer’s disease (AD) revealing strictly relationships between epigenetic and “classical” AD targets. Based on the reported connection among histone deacetylases (HDACs) and glycogen synthase kinase 3β (GSK-3β), herein we present the discovery and the biochemical characterization of the first-in-class hit compound able to exert promising anti-AD effects by modulating the targeted proteins in the low micromolar range of concentration. Compound 11 induces an increase in histone acetylation and a reduction of tau phosphorylation. It is nontoxic and protective against H(2)O(2) and 6-OHDA stimuli in SH-SY5Y and in CGN cell lines, respectively. Moreover, it promotes neurogenesis and displays immunomodulatory effects. Compound 11 shows no lethality in a wt-zebrafish model (

The term "5´ end mRNA artifact" refers to the incorrect assignment of the first AUG codon in an mRNA, due to the incomplete determination of its 5´ end sequence (Casadei et al., 2003). Since the '70s, the amino acid sequence of gene products has been routinely deduced from the nucleotide sequence of the relative cloned cDNA (DNA complementary to mRNA), according to rules for recognition of the start codon (first-AUG rule, optimal sequence context) and the genetic code (Kozak, 2002). All standard methods for the cloning of cDNA are affected by a potential inability to effectively clone the 5´ region of mRNA. This is due to the reverse transcriptase failure to extend first-strand cDNA along the full length of the mRNA template toward its 5´ end (Sambrook, 2001). The identification of a more complete mRNA 5´ end could reveal an additional upstream AUG – in-frame with the previously determined one – thus extending the predicted amino terminus sequence of the product and avoiding subsequent relevant errors in the experimental study of the relative cDNA (Casadei et al., 2003). The continuous incorporation of information derived from individual and large-scale cDNA sequencing projects, including those specifically designed to characterize mRNA 5´ end (Carninci et al., 1996; Suzuki et al., 2000; Porcel et al., 2004), in the last few years led to continuous improvement of completeness of mRNA reference sequences (e.g., RefSeq), and also to the corresponding protein coding sequences. However, genome browsers do not appear to systematically extract useful information from the ever-increasing vast quantity of EST (expressed sequence tag) data. To date, EST data remain invaluable due to significantly longer continuous RNA sequences they may provide in comparison with the very short fragments typically deposited in current high-throughput nucleotide sequencing databases. We previously used individual EST-based gene model refinement by classic in silico sequence analysis to revise the mRNA sequence of 109 human chromosome 21 protein-coding genes (Casadei et al., 2003). The success of this approach encouraged us to develop a piece of software ("5'_ORF_Extender" software) in order to automate the steps that were previously performed manually, applying it to the Danio rerio (zebrafish) genome (Frabetti et al., 2007). In the present work, we present a modified strategy able to analyze the much more numerous human sequences. Firstly, we fully revised the software algorithm by using pre-computed coordinates of the UCSC-downloaded RefSeqs and ESTs genome alignment data and specific UCSC-downloaded EST sequence entries. Furthermore, we adopted an original quality filter which was able to test if each single EST candidate with sequence information of possible use for extending a known mRNA, was attributed to the same locus of that mRNA by an updated, complete and embedded version of UniGene. Lastly, we automated data summarization for an analyzed genome. Following these improvements, parsing more than 7 million BLAT alignment, 5'_ORF_Extender 2.0 recognized a total of 477 loci, out of the 18,665 human loci represented in the mRNA reference set, as bona fide candidates for extension. Proof-of-concept confirmation was obtained by in vitro cloning and sequencing for GNB2L1 (guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1), QARS (glutaminyl-tRNA synthetase) and TDP2 (tyrosyl-DNA phosphodiesterase 2) cDNAs, and the consequences for the functional studies of these loci are discussed. In addition, we generated a list of 20,775 human mRNAs in which the presence of an in-frame stop codon upstream of the known start codon indicates completeness of the coding sequence at 5´ in the current form. Bibliografia: R. Casadei et al., mRNA 5’ region sequence incompleteness: a potential source of systematic errors in translation initiation codon assignment in human mRNAs, Gene 321 (2003) 185–193. M. Kozak, Pushing the limits of the scanning mechanism for initiation of translation, Gene 99 (2002) 1–34. P. Carninci et al., High-efficiency fulllength cDNA cloning by biotinylated CAP trapper, Genomics 37 (1996) 327–336. F. Frabetti et al., Systematic analysis of mRNA 5’ coding sequence incompleteness in Danio rerio: an automated EST-based approach, Biol. Direct 2 (2007) 34.

The aim of this work is to investigate the effect of a temperature increase on the behaviour of adult zebrafish (Danio rerio) maintained for 21 days at 34 °C (treatment) and 26 °C (control). The temperatures chosen are within the vital range of zebrafish and correspond to temperatures that this species encounters in the natural environment. Previous results showed that the same treatment affects the brain proteome and the behaviour of adult zebrafish by producing alterations in the proteins involved in neurotransmitter release and synaptic function and impairing fish exploratory behaviour. In this study, we have investigated the performance of treated and control zebrafish during environmental exploration by using four behavioural tests (novel tank diving, light and dark preference, social preference and mirror biting) that are paradigms for assessing the state of anxiety, boldness, social preference and aggressive behaviour, respectively. The results showed that heat treatment reduces anxiety and increases the boldness of zebrafish, which spent more time in potentially dangerous areas of the tank such as the top and the uncovered bright area and at a distance from the social group, thus decreasing protection for the zebrafish. These data suggest that the increase in ambient temperature may compromise zebrafish survival rate in the natural environment.

Experimental evidence suggests that environmental stress conditions can alter the expression of BDNF and that the expression of this neurotrophin influences behavioural responses in mammalian models. It has been recently demonstrated that exposure to 34 °C for 21 days alters the brain proteome and behaviour in zebrafish. The aim of this work was to investigate the role of BDNF in the nervous system of adult zebrafish under control and heat treatment conditions. For this purpose, zebrafish from three different genotypes (wild type, heterozygous BDNF+/− and knock out BDNF−/−) were kept for 21 days at 26 °C or 34 °C and then euthanized for brain molecular analyses or subjected to behavioural tests (Y-maze test, novel tank test, light and dark test, social preference test, mirror biting test) for assessing behavioural aspects such as boldness, anxiety, social preference, aggressive behaviour, interest for the novel environment and exploration. qRT-PCR analysis showed the reduction of gene expression of BDNF and its receptors after heat treatment in wild type zebrafish. Moreover, proteomic analysis and behavioural tests showed genotype- and temperature-dependent effects on brain proteome and behavioural responding. Overall, the absent expression of BDNF in KO alters (1) the brain proteome by reducing the expression of proteins involved in synapse functioning and neurotransmitter-mediated transduction; (2) the behaviour, which can be interpreted as bolder and less anxious and (3) the cellular and behavioural response to thermal treatment.

Histone deacetylase 8 (HDAC8) is a class 1 histone deacetylase and a member of the cohesin complex. HDAC8 is expressed in smooth muscles, but its expression in skeletal muscle has not been described. We have shown for the first time that HDAC8 is expressed in human and zebrafish skeletal muscles. Using RD/12 and RD/18 rhabdomyosarcoma cells with low and high differentiation potency, respectively, we highlighted a specific correlation with HDAC8 expression and an advanced stage of muscle differentiation. We inhibited HDAC8 activity through a specific PCI-34051 inhibitor in murine C2C12 myoblasts and zebrafish embryos, and we observed skeletal muscles differentiation impairment. We also found a positive regulation of the canonical Wnt signaling by HDAC8 that might explain muscle differentiation defects. These findings suggest a novel mechanism through which HDAC8 expression, in a specific time window of skeletal muscle development, positively regulates canonical Wnt pathway that is necessary for muscle differentiation.

Water temperature is an important environmental parameter influencing the distribution and the health of fishes and it plays a central role in ectothermic animals. The aim of this study is to determine the effects of environmental temperature on the brain proteome and the behavioural responses in zebrafish, a widely used animal model for environmental “omics” studies. Adult specimens of wild-type zebrafish were kept at 18 °C, 34 °C and 26 °C (control) for 21 days. Proteomic data revealed that several proteins involved in cytoskeletal organization, mitochondrial regulation and energy metabolism are differently regulated at the extreme temperatures. In particular, the expression of proteins associated to synapses and neurotransmitter release is down-regulated at 18 °C and 34 °C. In both thermal conditions, fish exhibited a reduced interest for the novel environment and an impairment of cognitive abilities during Y-Maze behavioural tests. The observed pathways of protein expression are possibly associated to functional alterations of the synaptic transmission that may result in cognitive functions impairment at central nervous system level as those revealed by behavioural tests. This study indicates that temperature variations can elicit biochemical changes that may affect fish health and behaviour. This combined approach provides insights into mechanisms supporting thermal acclimation and plasticity in fishes. Significance Environmental temperature variation may impact on all levels of biological life. Understanding the impact of thermal variation on the nervous system and animal behaviour is of primary importance since the results obtained can be applied from the ecological to the biomedical fields.

CYYR1 (Cysteine/tyrosine-rich 1) cloned on human chromosome 21 defines a new family of highly conserved vertebrate-specific genes1,2. The analysis of the human locus revealed the presence of a multitranscript-system that includes alternative spliced isoforms and one ncRNA gene overlapping CYYR1 in antisense orientation3. Original results suggest the need of further investigations in order to verify a putative role of CYYR1 in the tumorigenic process, caused by dysfunction of cell differentiation and possibly related to the Hh pathway4; to date, the specific function of the CYYR1 product is still unknown. The zebrafish cyyr1 is present in single copy and maintains almost 58% of identity with human protein therefore, we decided to perform a full characterization of cyyr1 expression and function using zebrafish as model system. WISH approach defined a broad expression in central nervous system (CNS), somites and muscles during somitogenesis and at 24-48 hpf. The cyyr1 knock-down with two different MOs targetting the ATG and the first splice-site of the transcript, affected both CNS and muscle development with a significant rescue in embryo co-injected with cyyr1 mRNA. Defects were also evident in ciliated cells of neuromast of the lateral line. Morphologically, the cyyr1-MOs injected embryos display some features of embryos inhibited for the Hh pathway through injection of the lefty mRNA and cyyr1 expression was significantly inhibited following Hh inhibition. Interestingly, the injection of cyyr1 mRNA was able to partially rescue Hh-defective phenotype in embryos at 24 hpf. Results obtained through immunofluorescent staining, qPCR and western blotting, support a role for cyyr1 in primary myogenesis probably downstream of Hh pathway. 1. Vitale L et al. Gene 2002, 290:141-51. 2. Casadei R et al. Gene Expr Patterns 2011, 11: 271-6. 3. Casadei R et al. Mol Biol Rep 2014, 41:6025-38. 4. Xu J et al. Genetics 2006, 174:735-52.

The understanding of the genetic basis of the PD and the correlation between genotype and phenotype has revolutionized knowledge about the pathogenetic mechanisms of neurodegeneration, opening up exciting new therapeutic and neuroprotective perspectives. Genomic knowledge for PD is still very open and can provide a good start for studies of the molecular mechanisms that underlie the gene expression variations and the epigenetic mechanisms that may contribute to the complex and characteristic phenotype of PD. Here we use the software TRAM (Transcriptome Mapper), to analyse publicly available microarray data of PD patients and controls substantia nigra, to identify chromosomal segments (Map mode) and gene clusters (Cluster mode) which are biologically relevant in the two different conditions. TRAM integrates original methods for parsing, normalizing, mapping and statistically analyzing expression data; in addition, it is able to easily generate maps showing differential expression between two sample groups, relative to two different biological conditions. We performed a systematic meta-analysis of 143 samples from pool A (patients with PD) and 119 samples from pool B (healthy controls), for a total of respectively 4,128,764 data points (gene expression value) and 3,417,633 data points, relative to 37,580 distinct loci for wich A/B ratio value was determinable. Results obtained included 5 significantly over-expressed segments and 90 over/under-expressed clusters. A list of statistically significant over/under-expressed genes has been generated, including coding genes, ncRNAs and uncharacterized transcripts. This study offers a new approach for the regional analysis of gene expression in neurodegenerative diseases.

Down syndrome critical region gene 1-like 2 (DSCR1L2) belongs to the human DSCR1-like gene family, which also includes DSCR1 and DSCR1L1. Both DSCR1 and DSCR1L1 proteins interact with calcineurin, a calcium/calmodulin-dependent phosphatase. To date, no interactor has been described for DSCR1L2. The aim of this work was to perform a first functional study of DSCR1L2 using yeast two-hybrid analysis conducted on a human heart cDNA library. Here, we report the interaction between DSCR1L2 and the human cardiac troponin I (TNNI3), the heart-specific inhibitory subunit of the troponin complex, a central component of the contractile apparatus. This interaction was confirmed by both yeast cotransformation and GST (glutathione-sepharose transferase) fusion protein assay. Moreover, a new DSCR1L2 mRNA isoform, generated by alternative splicing, was identified and cloned in different tissues: it lacks two central exons, encoding the most conserved domains among the DSCR1-like protein family. A quantitative relative reverse transcription-polymerase chain reaction (RT-PCR) assay showed that in heart tissue the normalized expression level ratio for DSCR1L2 and DSCR1L2-E2E5 mRNA isoforms is 3.5 : 1, respectively. The yeast cotransformation and GST fusion protein assay demonstrated the interaction between this new DSCR1L2 variant and the human cardiac troponin I and the prominent role of DSCR1L2 exon 2 in determining binding between both DSCR1L2 isoforms and TNNI3. These data indicate an entirely new role for a DSCR1-like family gene, suggesting a possible involvement of DSCR1L2 in cardiac contraction.

Summary: Extracting the desired data from a database entry for later analysis is a constant need in the biological sequence analysis community; GeneRecords 1.0 is a solution for GenBank biological flat file parsing, as it implements a structured representation of each feature and feature qualifier in GenBank following import in a common database managing system usable in a personal computer (Macintosh and Windows environments). This collection of related databases enables the local management of GenBank records, allowing indexing, retrieval and analysis of both information and sequences on a personal computer. Availability: the current release, including the FileMaker Pro runtime application (built for Windows and Macintosh environments), is freely available at http://apollo11.isto.unibo.it/software/

La didattica della Biologia è un percorso affascinante. Oggi le conoscenze scientifiche raggiunte in questo campo a livello molecolare, cellulare e degli organismi, ci propongono nuovi orizzonti. Le sempre maggiori informazioni scientifiche, d’altro canto, sfruttano molte risorse e fonti per raggiungere chiunque voglia conoscere nuovi aspetti del mondo biologico che lo circonda e che lo riguarda da vicino. L’approccio ad una materia così complessa può però comportare il rischio di una inutile dispersione di energia nel tentativo di approfondire ognuno dei tanti aspetti e contenuti, o viceversa, rendere banale e superficiale lo studio e dunque meno interessante ed incisivo il percorso conoscitivo degli studenti. In base a queste premesse, un buon libro deve essere necessariamente una sintesi aggiornata della materia, ma anche uno strumento in grado di aiutare i docenti ad insegnare e gli studenti ad apprendere. Questo testo nasce proprio dall’idea di rivisitare il testo di Campbell e Reece, Biologia 8/Ed., un ottimo testo americano, modulando le parti che più calzano ai programmi degli studi biomedici di molti corsi di laurea, centrando l’attenzione alla biologia umana. Il corpo del testo si sviluppa attraverso argomenti di biologia molecolare, citologia e fisiologia cellulare, nonché biologia animale con particolare riferimento ai processi endocrini, riproduttivi e di sviluppo. Un importante sforzo è stato fatto nell’originale inserimento di argomenti di Genetica medica. Questi contenuti rendono l’opera ancora più flessibile per i programmi che da anni integrano corsi di biologia applicata agli studi medici e la genetica formale da un lato, con la genetica umana e un’introduzione alla clinica dall’altro. Questa integrazione diventa un potente ausilio nello specifico in corsi di laurea come quello dell’Infermieristica e colma una lacuna da tempo sottolineata da studenti e docenti. Gli studenti troveranno in Biologia e genetica un utile sussidio alla propria preparazione nella chiarezza espositiva, nei contenuti aderenti ai programmi svolti a lezione e in puntuali verifiche di apprendimento. I docenti avranno modo di rimandare a un testo completo e organico nelle sue parti. Il testo si propone come possibile riferimento in corsi di laurea quali scienze motorie, farmacia, biologia e, in generale, nelle lauree delle professioni sanitarie.

Various tools have been developed to perform global gene expression profile data analysis, to search for specific chromosomal regions whose features meet defined criteria as well as to study neighbouring gene expression. However, most of these tools are tailored for a specific use in a particular context (e.g. they are species-specific, or limited to a particular data format) and they typically accept only gene lists as an input. TRAM (Transcriptome Mapper) is a new general software tool that allows the simple generation and analysis of quantitative transcriptome maps, starting from any source listing gene expression values for a given gene set (e.g. expression microarrays), implemented as a relational database. It includes a parser able to assign univocal and updated gene symbols to gene identifiers from different data sources, as well as to perform intra-sample and inter-sample data normalization methods, including an original variant of quantile normalization (scaled quantile) useful to normalize data from platforms with highly different numbers of investigated genes. When in 'Map' mode, the software generates a quantitative representation of the transcriptome of a sample (or of a pool of samples) and identifies if chromosomal segments of defined length are over/under-expressed compared to the desired threshold. When in 'Cluster' mode, the software searches the genome for a set of over/under-expressed consecutive genes. Statistical significance for all results is calculated with respect to genes localized on the same chromosome or to all genome genes. Transcriptome maps, showing differential expression between two sample groups, relative to two different biological conditions, may be easily generated. We present the results of a test biological model, based on a meta-analysis comparison between a human CD34+ hematopoietic progenitor cells sample pool and a megakaryocytic cells sample pool, identifying biologically relevant chromosomal segments and gene clusters with differential expression during the differentiation toward megakaryocyte. The large agreement with classical biological knowledge about megakaryocytopoiesis of TRAM results, obtained without any a priori specific assumption, shows that TRAM can perform integrated analysis of expression data from multiple platforms producing high confidence lists of over/under-expressed chromosomal segments and clustered genes. TRAM is the first complete software usable in a personal computer (Macintosh and Windows environments) designed to create, and statistically analyze, quantitative transcriptome maps, based on gene expression data from multiple sources. In conjunction with our previous implementation of a GenBank [1, 2] and UniGene [3] formats full parsing systems, TRAM may also contribute to the building of a novel, relational, multi-purpose, user-friendly and modular platform for the large-scale integrated analysis of genomic and post-genomic data.