Biomedical subjects

Giorgio Valle

Publications and source records attributed to Giorgio Valle.

At least 19 recordsLinked to original sources

PubMed2006

The LGI1/epitempin gene encodes two protein isoforms differentially expressed in human brain.

The leucine-rich, glioma inactivated 1 (LGI1)/Epitempin gene has been linked to two phenotypes as different as gliomagenesis and autosomal dominant lateral temporal epilepsy. Its function and the biochemical features of the encoded protein are unknown. We characterized the LGI1/Epitempin protein product by western blot analysis of mouse and human brain tissues. Two proteins of about 60 and 65 kDa were detected by an anti-LGI1 antibody within the expected molecular mass range. The two proteins appeared to reside in different subcellular compartments, as they were fractionated by differential centrifugation. The specificity of both polypeptides was validated by cell transfection assay and mass spectrometry analysis. Immunoblot analysis of protein distribution in various zones of the human brain revealed variable amounts of both proteins. Notably, these proteins were more abundant in the temporal neocortex than in the hippocampus, the difference in abundance of the 65-kDa product being particularly pronounced. These results suggest that the two protein isoforms encoded by LGI1/Epitempin are differentially expressed in the human brain, and that higher expression levels of these proteins in the lateral temporal cortex may underlie the susceptibility of this brain region to the epileptogenic effects of LGI1/Epitempin mutations.

Aged, 80 and over↗

PubMed2006

Piezophilic adaptation: a genomic point of view.

Two-thirds of Earth's surface is covered by oceans, yet the study of this massive integrated living system is still in its infancy. Various environmental variables, such as high salinity, low and changeable nutrient availability and depth-correlated gradients of light, temperature, nutrients and pressure shape the diversity, physiology and ecology of marine species. As oceans present an average depth of 3800 m, deep-sea ecosystems represent the most common marine ecological niche. One of the key environment variables that influences the life and evolution of deep-sea organisms is high pressure. This extreme widespread condition requires specific adaptations, the nature of which remains largely unknown. Recent advances in genomic approaches, such as in sequencing technologies and global expression profiling, are rapidly increasing the data available to understand microbial evolution, biochemistry, physiology and diversity. This review summarises the analysis of the results published so far about microbial high pressure adaptation from a genomic point of view. Understanding high pressure adaptation mechanisms is not just a scientific exercise but has important biotechnological implications. For example, hydrostatic pressure is a reality for food science and technology, both for food preparation and preservation. An understanding of the effects of pressure on biomolecules will expand its use in the medical, industrial and biotechnological fields.

Acclimatization↗

PubMed2006

Haplogroup effects and recombination of mitochondrial DNA: novel clues from the analysis of Leber hereditary optic neuropathy pedigrees.

The mitochondrial DNA (mtDNA) of 87 index cases with Leber hereditary optic neuropathy (LHON) sequentially diagnosed in Italy, including an extremely large Brazilian family of Italian maternal ancestry, was evaluated in detail. Only seven pairs and three triplets of identical haplotypes were observed, attesting that the large majority of the LHON mutations were due to independent mutational events. Assignment of the mutational events into haplogroups confirmed that J1 and J2 play a role in LHON expression but narrowed the association to the subclades J1c and J2b, thus suggesting that two specific combinations of amino acid changes in the cytochrome b are the cause of the mtDNA background effect and that this may occur at the level of the supercomplex formed by respiratory-chain complexes I and III. The families with identical haplotypes were genealogically reinvestigated, which led to the reconnection into extended pedigrees of three pairs of families, including the Brazilian family with its Italian counterpart. The sequencing of entire mtDNA samples from the reconnected families confirmed the genealogical reconstruction but showed that the Brazilian family was heteroplasmic at two control-region positions. The survey of the two sites in 12 of the Brazilian subjects revealed triplasmy in most cases, but there was no evidence of the tetraplasmy that would be expected in the case of mtDNA recombination.

DNA, Mitochondrial↗

PubMed2006

Quantitative proteomic comparison of rat mitochondria from muscle, heart, and liver.

Mitochondria, through oxidative phosphorylation, are the primary source of energy production in all tissues under aerobic conditions. Although critical to life, energy production is not the only function of mitochondria, and the composition of this organelle is tailored to meet the specific needs of each cell type. As an organelle, the mitochondrion has been a popular subject for proteomic analysis, but quantitative proteomic methods have yet to be applied to tease apart subtle differences among mitochondria from different tissues or muscle types. Here we used mass spectrometry-based proteomics to analyze mitochondrial proteins extracted from rat skeletal muscle, heart, and liver tissues. Based on 689 proteins identified with high confidence, mitochondria from the different tissues are qualitatively quite similar. However, striking differences emerged from the quantitative comparison of protein abundance between the tissues. Furthermore we applied similar methods to analyze mitochondrial matrix and intermembrane space proteins extracted from the same mitochondrial source, providing evidence for the submitochondrial localization of a number of proteins in skeletal muscle and liver. Several proteins not previously thought to reside in mitochondria were identified, and their presence in this organelle was confirmed by protein correlation profiling. Hierarchical clustering of microarray expression data provided further evidence that some of the novel mitochondrial candidates identified in the proteomic survey might be associated with mitochondria. These data reveal several important distinctions between mitochondrial and submitochondrial proteomes from skeletal muscle, heart, and liver tissue sources. Indeed approximately one-third of the proteins identified in the soluble fractions are associated predominantly to one of the three tissues, indicating a tissue-dependent regulation of mitochondrial proteins. Furthermore a small percentage of the mitochondrial proteome is unique to each tissue.

Amino Acid Sequence↗

PubMed2005

Functional insights from the structural modelling of a small Fe-hydrogenase.

Recently, a novel Fe-hydrogenase from a high rate of hydrogen producing Enterobacter cloacae strain IIT-BT08 was identified and partially characterized. This 147 residue protein was found to be much smaller than previously known Fe-hydrogenases, yet retaining a high catalytic activity. We predicted the structure of this protein and found it to be structurally similar to one of the two sub-domains containing the catalytic H-cluster so far jointly present in all other Fe-hydrogenases. This novel architecture allows a tentative explanation of protein function with the high rate of catalytic activity being due to a missing regulatory sub-domain, presumably allowing higher enzymatic activity at the cost of greater exposure to oxygen inactivation. This new insight may improve our understanding of the molecular and functional organization of other, more complex Fe-hydrogenases.

Amino Acid Sequence↗

PubMed2005

Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains.

BACKGROUND: Oceans cover approximately 70% of the Earth's surface with an average depth of 3800 m and a pressure of 38 MPa, thus a large part of the biosphere is occupied by high pressure environments. Piezophilic (pressure-loving) organisms are adapted to deep-sea life and grow optimally at pressures higher than 0.1 MPa. To better understand high pressure adaptation from a genomic point of view three different Photobacterium profundum strains were compared. Using the sequenced piezophile P. profundum strain SS9 as a reference, microarray technology was used to identify the genomic regions missing in two other strains: a pressure adapted strain (named DSJ4) and a pressure-sensitive strain (named 3TCK). Finally, the transcriptome of SS9 grown under different pressure (28 MPa; 45 MPa) and temperature (4 degrees C; 16 degrees C) conditions was analyzed taking into consideration the differentially expressed genes belonging to the flexible gene pool. RESULTS: These studies indicated the presence of a large flexible gene pool in SS9 characterized by various horizontally acquired elements. This was verified by extensive analysis of GC content, codon usage and genomic signature of the SS9 genome. 171 open reading frames (ORFs) were found to be specifically absent or highly divergent in the piezosensitive strain, but present in the two piezophilic strains. Among these genes, six were found to also be up-regulated by high pressure. CONCLUSION: These data provide information on horizontal gene flow in the deep sea, provide additional details of P. profundum genome expression patterns and suggest genes which could perform critical functions for abyssal survival, including perhaps high pressure growth.

Atmospheric Pressure↗

PubMed2004

RAP: a new computer program for de novo identification of repeated sequences in whole genomes.

MOTIVATION: DNA repeats are a common feature of most genomic sequences. Their de novo identification is still difficult despite being a crucial step in genomic analysis and oligonucleotides design. Several efficient algorithms based on word counting are available, but too short words decrease specificity while long words decrease sensitivity, particularly in degenerated repeats. RESULTS: The Repeat Analysis Program (RAP) is based on a new word-counting algorithm optimized for high resolution repeat identification using gapped words. Many different overlapping gapped words can be counted at the same genomic position, thus producing a better signal than the single ungapped word. This results in better specificity both in terms of low-frequency detection, being able to identify sequences repeated only once, and highly divergent detection, producing a generally high score in most intron sequences. AVAILABILITY: The program is freely available for non-profit organizations, upon request to the authors. CONTACT: giorgio.valle@unipd.it SUPPLEMENTARY INFORMATION: The program has been tested on the Caenorhabditis elegans genome using word lengths of 12, 14 and 16 bases. The full analysis has been implemented in the UCSC Genome Browser and is accessible at http://genome.cribi.unipd.it.

Algorithms↗

PubMed2004

The SSEA server for protein secondary structure alignment.

SUMMARY: We present a web server that computes alignments of protein secondary structures. The server supports both performing pairwise alignments and searching a secondary structure against a library of domain folds. It can calculate global and local secondary structure element alignments. A combination of local and global alignment steps can be used to search for domains inside the query sequence or help in the discrimination of novel folds. Both the SCOP and PDB fold libraries, clustered at 95 and 40% sequence identity, are available for alignment. AVAILABILITY: The web server interface is freely accessible to academic users at http://protein.cribi.unipd.it/ssea/. The executable version and benchmarking data are available from the same web page.

Algorithms↗

PubMed2004

The Ankrd2 protein, a link between the sarcomere and the nucleus in skeletal muscle.

Ankrd2 may be a link between the sarcomere and the nucleus; a similar role has recently been proposed for CARP that has a high level of structural and functional conservation with Ankrd2. Both Ankrd2 and CARP are involved in striated muscle hypertrophy. The mechanism by which muscle stretch is sensed and signals are transduced is still unknown; however, Ankrd2 and CARP could play similar roles in pathways leading to hypertrophy, the triggering mechanisms being heart pressure overload monitored by CARP and mechanical stretch in skeletal muscle monitored by Ankrd2. Recently Ankrd2 and CARP have been proposed as members of a family of muscle ankyrin repeat proteins (MARPs) that form a complex with titin, myopalladin and calpain protease p94, involved in signaling and regulation of gene expression in response to muscle stress. Here, we show that Ankrd2 is able to interact with the Z-disc protein telethonin as well as being able to interact with three transcription factors: YB-1, PML and p53. Ankrd2 binding to the ubiquitous transcription factor YB-1 can be demonstrated both in vitro and in vivo; this is not very surprising, since a similar interaction was previously described for CARP. However, the interactions with PML and p53 are unexpected new findings, with interesting implications in the Ankrd2 signaling cascade. Ankrd2 co-localizes with the transcriptional co-activator and co-repressor PML in nuclear bodies (NBs) in human myoblasts as detected by confocal immunofluorescence. Interestingly, we show that Ankrd2 not only binds the tumor suppressor protein p53 both in vitro and in vivo but also enhances the up-regulation of the p21(WAFI/CIPI) promoter by p53. Therefore, our findings strengthen the hypothesis that Ankrd2 may be involved in sensing stress signals and linking these to muscle gene regulation.

CCAAT-Enhancer-Binding Proteins↗

PubMed2004

The mitochondrial genome of the house centipede scutigera and the monophyly versus paraphyly of myriapods.

Recent advances in molecular phylogenetics are continuously changing our perception of the phylogenetic relationships among the main arthropod lineages: crustaceans, hexapods, chelicerates, and myriapods. Besides the intrinsic interest in unraveling the evolution of the largest animal phylum, these studies are basic to an understanding of one of the major transitions in animal evolution-i.e., the conquest of land with all its associated structural and functional adaptations. Myriapods have been traditionally considered the closest relatives of hexapods, thus implying only one origin of terrestriality for the tracheate lineage, but this view is now challenged by molecular evidence. Sequence data available to date for centipedes and millipedes are very limited, and the taxon sampling is strongly biased. The most critical gap was the scutigeromorph centipedes, which are the sister group to all remaining Chilopoda from which they probably diverged in the Silurian if not earlier. We obtained the first complete mitochondrial sequence for a representative of this clade, the house centipede. In our phylogenetic analyses of the protein-coding genes in this mitochondrial genome, along with 16 further ones representing the other major arthropod clades plus two outgroups, the myriapods formed a clade with the chelicerates. This implies that water-to-land transition occurred at least three times (hexapods, myriapods, arachnids) during the evolution of the Arthropoda. In addition, in contrast to all previous studies, our best supported topologies favor paraphyly of the myriapods with respect to the chelicerates. This would increase to four the main events of land colonization in arthropods (once for centipedes, once for millipedes).

Animals↗

PubMed2004

Extensive gene order rearrangement in the mitochondrial genome of the centipede Scutigera coleoptrata.

We describe the complete mitochondrial genome of the house centipede Scutigera coleoptrata. Its gene order is unique among characterized arthropod mitochondrial genomes. Comparison to the gene order in the horseshoe crab mtDNA implies 10 or more translocations. By extending comparisons to 30 arthropod mitochondrial genomes plus two outgroups, we identify two different patterns of gene order change. The first, only affecting position and orientation of tRNAs, is much more frequent than the second, which also involves protein encoding and ribosomal genes. The analysis of the same data set using available algorithms for phylogenetic reconstruction based on gene order results in unreliable trees. This indicates that the current methods for analyzing gene order rearrangement are not suitable for wide-ranging phylogenetic studies.

Animals↗

PubMed2003

PRIMEX: rapid identification of oligonucleotide matches in whole genomes.

SUMMARY: PRIMEX (PRImer Match EXtractor) can detect oligonucleotide sequences in whole genomes, allowing for mismatches. Using a word lookup table and server functionality, PRIMEX accepts queries from client software and returns matches rapidly. We find it faster and more sensitive than currently available tools. AVAILABILITY: Running applications and source code have been made available at http://bioinformatics.cribi.unipd.it/primex

Algorithms↗

PubMed2003

Mutations in Cypher/ZASP in patients with dilated cardiomyopathy and left ventricular non-compaction.

OBJECTIVES: We evaluated the role of Cypher/ZASP in the pathogenesis of dilated cardiomyopathy (DCM) with or without isolated non-compaction of the left ventricular myocardium (INLVM). BACKGROUND: Dilated cardiomyopathy, characterized by left ventricular dilation and systolic dysfunction with signs of heart failure, is genetically transmitted in 30% to 40% of cases. Genetic heterogeneity has been identified with mutations in multiple cytoskeletal and sarcomeric genes causing the phenotype. In addition, INLVM with a hypertrophic dilated left ventricle, ventricular dysfunction, and deep trabeculations, is also inherited, and the genes identified to date differ from those causing DCM. Cypher/ZASP is a newly identified gene encoding a protein that is a component of the Z-line in both skeletal and cardiac muscle. METHODS: Diagnosis of DCM was performed by echocardiogram, electrocardiogram, and physical examination. In addition, levels of the muscular isoform of creatine kinase were measured to evaluate for skeletal muscle involvement. Cypher/ZASP was screened by denaturing high performance liquid chromatography (DHPLC) and direct deoxyribonucleic acid sequencing. RESULTS: We identified and screened 100 probands with left ventricular dysfunction. Five mutations in six probands (6% of cases) were identified in patients with familial or sporadic DCM or INLVM. In vitro studies showed cytoskeleton disarray in cells transfected with mutated Cypher/ZASP. CONCLUSIONS: These data suggest that mutated Cypher/ZASP can cause DCM and INLVM and identify a mechanistic basis.

Adaptor Proteins, Signal Transducing↗

PubMed2003

Pattern recognition in gene expression profiling using DNA array: a comparative study of different statistical methods applied to cancer classification.

Large-scale parallel measurements of the expression of many thousands genes are now available with high-density array made with collections of cDNA fragments, or oligonucleotide corresponding to different transcripts. These technologies have been applied to cancer investigations since the availability of such a large number of markers makes DNA array a powerful diagnostic tool for tumour and patient classification. Over the last two years, a series of computational tools have been developed for the analysis of different aspects of gene profiling. Our work tries to compare a series of supervised statistical techniques on the basis of their ability to correctly classify different types of tumours. A simulation approach was initially used to control the huge source of variation among and between patients, and to evaluate the ability of algorithms to classify tumours in relation to different types of experimental variables. Different techniques for reduction of data dimension were then added to the discriminant analysis and compared according to their ability to capture the main genetic information. The simulation results have been tested by applying the selected classification algorithms to two experimental microarray datasets of human cancers, and by measuring the correspondent rates of misclassification. Our analyses identify in these datasets a series of genes principally involved in tumour characterization. The functional role of these discriminant transcripts is discussed.

Algorithms↗

PubMed2003

TRAIT (TRAnscript Integrated Table): a knowledgebase of human skeletal muscle transcripts.

TRAIT is a knowledgebase integrating information on transcripts with related data from genome, proteins, ortholog genes and diseases. It was initially built as a system to manage an EST-based gene discovery project on human skeletal muscle, which yielded over 4500 independent sequence clusters. Transcripts are annotated using automatic as well as manual procedures, linking known transcripts to public databases and unknown transcripts to tables of predicted features. Data are stored in a MySQL database. Complex queries are automatically built by means of a user-friendly web interface that allows the concurrent selection of many fields such as ontology, expression level, map position and protein domains. The results are parsed by the system and returned in a ranked order, in respect to the number of satisfied criteria.

Database Management Systems↗

PubMed2003

Human MYO18B, a novel unconventional myosin heavy chain expressed in striated muscles moves into the myonuclei upon differentiation.

We have characterized a novel unconventional myosin heavy chain, named MYO18B, that appears to be expressed mainly in human cardiac and skeletal muscles and, at lower levels, in testis. MYO18B transcript is detected in all types of striated muscles but at much lower levels compared to class II sarcomeric myosins, and it is up regulated after in vitro differentiation of myoblasts into myotubes. Phylogenetic analysis shows that this myosin belongs to the recently identified class XVIII, however, unlike the other member of this class, it seems to be unique to Vertebrate since it contains two large amino acid domains of unknown function at the N and C-termini. Immunolocalization of MYO18B protein in skeletal muscle cells shows that this myosin heavy chain is located in the cytoplasm of undifferentiated myoblasts. After in vitro differentiation into myotubes, a fraction of this protein is accumulated in a subset of myonuclei. This nuclear localization was confirmed by immunofluorescence experiments on primary cardiomyocytes and adult muscle sections. In the cytoplasm MYO18B shows a punctate staining, both in cardiac and skeletal fibers. In some cases, cardiomyocytes show a partial sarcomeric pattern of MYO18B alternating that of alpha-actinin-2. In skeletal muscle the cytoplasmic MYO18B results much more evident in the fast type fibers.

Animals↗

PubMed2003

Autosomal dominant lateral temporal epilepsy: clinical spectrum, new epitempin mutations, and genetic heterogeneity in seven European families.

PURPOSE: [corrected] To describe the clinical and genetic findings of seven additional pedigrees with autosomal dominant lateral temporal epilepsy (ADLTE). METHODS: A personal and family history was obtained from each affected and unaffected member, along with a physical and neurologic examination. Routine and sleep EEGs, computed tomography (CT), or magnetic resonance imaging (MRI) were performed in almost all the patients. DNAs from family members were typed with several microsatellite markers localized on either side of LGI1 at 10q24 and screened for LGI1 mutations. RESULTS: The seven families included a total of 34 affected individuals (10 deceased). The age at onset ranged between 8 and 50 years (average, 22 years). Twenty-six patients had clear-cut focal (elementary, complex, or secondarily generalized) seizures, characterized by prominent auditory auras in 68% of the cases. Less frequent ictal symptoms were visual, psychic, or aphasic seizures, the latter occurring in isolation in one family. The attacks were rare and well controlled by antiepileptic drug treatment but recurred after drug discontinuation. Interictal EEGs were usually unrevealing. MRI or CT scans were negative. Analysis of LGI1/Epitempin exons failed to show mutations in three pedigrees. Linkage analysis strongly suggested exclusion of linkage in one of these families. We found two novel missense mutations, a T-->C substitution in exon 6 at position 598, and a T-->A transition in exon 8 at position 1295, the latter being detected in a family with aphasic seizures. CONCLUSIONS: Our data confirm the inclusion of aphasic seizures within the ADLTE clinical spectrum, suggest the existence of locus heterogeneity in ADLTE, and provide new familial cases with LGI1 missense mutations associated with the disease.

Adolescent↗

PubMed2003

Simple consensus procedures are effective and sufficient in secondary structure prediction.

We have analyzed the performance of majority voting on minimal combination sets of three state-of-the-art secondary structure prediction methods in order to obtain a consensus prediction. Using three large benchmark sets from the EVA server, our results show a significant improvement in the average Q3 prediction accuracy of up to 1.5 percentage points by consensus formation. The application of an additional trivial filtering procedure for predicted secondary structure elements that are too short, does not significantly affect the prediction accuracy. Our analysis also provides valuable insight into the similarity of the results of the prediction methods that we combine as well as the higher confidence in consistently predicted secondary structure.

Computational Biology↗