Biomedical subjects

Monica Santamaria

Publications and source records attributed to Monica Santamaria.

9 recordsLinked to original sources

PubMed2025

Establishing the ELIXIR Microbiome Community.

Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples. In particular, experimental approaches such as metagenomics, metabarcoding, metatranscriptomics and metaproteomics have provided profound insights into the vast, hitherto unknown, microbial biodiversity. The ELIXIR Marine Metagenomics Community, initiated amongst researchers focusing on marine microbiomes, has concentrated on promoting standards around microbiome-derived sequence analysis, as well as understanding the gaps in methods and reference databases, and identifying solutions to the computational overheads of performing such analyses. Nevertheless, the methods used and the challenges faced are not confined to marine microbiome studies, but are broadly applicable to other biomes. Thus, expanding this Marine Metagenomics Community to a more inclusive ELIXIR Microbiome Community will enable it to encompass a broader range of biomes and link expertise across 'omics technologies. Furthermore, engaging with a large number of researchers will improve the efficiency and sustainability of bioinformatics infrastructure and resources for microbiome research (standards, data, tools, workflows, training), which will enable a deeper understanding of the function and taxonomic composition of the different microbial communities.

Computational Biology↗

PubMed2006

Methylthioadenosine reverses brain autoimmune disease.

OBJECTIVE: To assess the immunomodulatory activity of methylthioadenosine (MTA) in rodent experimental autoimmune encephalomyelitis (EAE) and in patients with multiple sclerosis. METHODS: We studied the effect of intraperitoneal MTA in the acute and chronic EAE model by quantifying clinical and histological scores and by performing immunohistochemistry stains of the brain. We studied the immunomodulatory effect of MTA in lymphocytes from EAE animals and in peripheral blood mononuclear cells from healthy control subjects and multiple sclerosis patients by assessing cell proliferation and cytokine gene expression, by real-time polymerase chain reaction, and by nuclear factor-kappaB modulation by Western blot. RESULTS: We found that MTA prevents acute EAE and, more importantly, reverses chronic-relapsing EAE. MTA treatment markedly inhibited brain inflammation and reduced brain damage. Administration of MTA suppressed T-cell activation in vivo and in vitro, likely through a blockade in T-cell signaling resulting in the prevention of inhibitor of kappa B (IkappaB-alpha) degradation and in the impaired activation transcription factor nuclear factor-kappaB. Indeed, MTA suppressed the production of proinflammatory genes and cytokines (interferon-gamma, tumor necrosis factor-alpha, and inducible nitric oxide synthase) and increased the production of antiinflammatory cytokines (interleukin-10). INTERPRETATION: MTA has a remarkable immunomodulatory activity and may be beneficial for multiple sclerosis and other autoimmune diseases.

Adult↗

PubMed2006

Human mtDNA site-specific variability values can act as haplogroup markers.

Sequencing of entire human mtDNA genomes has become rapid and efficient, leading to the production of a great number of complete mtDNA sequences from a wide range of human populations. We introduce here a new statistical approach for classifying mtDNA nucleotide sites, simply by comparing the mean simple deviation (MSD) of their specific variability values estimated on continent-specific dataset sequences, without the need for any reference sequence. Excellent correspondence was observed between sites with the highest MSD values and those marking known mtDNA haplogroups. This in turn supports the classification of 81 sites (23 in Africa, eight in Asia, eight in Europe, 34 in Oceania, and eight in America) as novel markers of 47 mtDNA haplogroups not yet identified by phylogeographic studies. Not only does this approach allow refinement of mtDNA phylogeny, an essential requirement also for mitochondrial disease studies, but may greatly facilitate the discrimination of candidate disease-causing mutations from haplogroup-specific polymorphisms in mtDNA sequences of patients affected by mitochondrial disorders.

DNA Mutational Analysis↗

PubMed2006

S-adenosylmethionine regulates cytoplasmic HuR via AMP-activated kinase.

BACKGROUND & AIMS: After liver injury, hepatic S-adenosylmethionine (SAM) content decreases, and the blockage this molecule imposes on hepatocyte proliferation is released, facilitating liver regeneration. This activity of SAM is important for normal liver function because mice deficient in hepatic SAM display abnormal liver regeneration and develop hepatocellular carcinoma. How SAM regulates hepatocyte growth is unclear, but because SAM blocks hepatocyte growth factor (HGF)-induced cyclin D1 expression and DNA synthesis without affecting HGF-induced extracellular signal-regulated kinase phosphorylation, the mitogen-activated protein kinase (MAPK) pathway is probably not the target. METHODS: The effects of SAM on AMPK, HuR localization were assessed in rat hepatocytes after HGF, AICAR, and SAM treatment. RESULTS: We show here that HGF and 5-aminoimidazole-4-carboxamide-riboside (AICAR), an activator of AMP-activated protein kinase (AMPK), induce the phosphorylation of AMPK in hepatocytes and that SAM blocks this process. We also show that HGF- and AICAR-induced AMPK activation stimulate the transport from nucleus to cytoplasm of HuR, an RNA-binding protein that increases the half-life of target mRNA such as cyclin A2, and that SAM blocks this process. We found that, in hepatocytes, AICAR increases HuR binding to cyclin A2 messenger RNA (mRNA) as well as the expression and stability of this mRNA and that SAM blocks these events. Consistently, we found that AICAR induces hepatocyte proliferation and that SAM blocks this effect. Finally, we found that liver AMPK phosphorylation, cytoplasmic HuR, and binding of HuR to HuR-target mRNA and the steady-state levels of these mRNA are increased in knockout mice deficient in hepatic SAM. CONCLUSIONS: Our results yield novel insights about the mechanism by which SAM inhibits cell-cycle progression in the liver.

AMP-Activated Protein Kinases↗

PubMed2005

HmtDB, a human mitochondrial genomic resource based on variability studies supporting population genetics and biomedical research.

BACKGROUND: Population genetics studies based on the analysis of mtDNA and mitochondrial disease studies have produced a huge quantity of sequence data and related information. These data are at present worldwide distributed in differently organised databases and web sites not well integrated among them. Moreover it is not generally possible for the user to submit and contemporarily analyse its own data comparing them with the content of a given database, both for population genetics and mitochondrial disease data. RESULTS: HmtDB is a well-integrated web-based human mitochondrial bioinformatic resource aimed at supporting population genetics and mitochondrial disease studies, thanks to a new approach based on site-specific nucleotide and aminoacid variability estimation. HmtDB consists of a database of Human Mitochondrial Genomes, annotated with population data, and a set of bioinformatic tools, able to produce site-specific variability data and to automatically characterize newly sequenced human mitochondrial genomes. A query system for the retrieval of genomes and a web submission tool for the annotation of new genomes have been designed and will soon be implemented. The first release contains 1255 fully annotated human mitochondrial genomes. Nucleotide site-specific variability data and multialigned genomes can be downloaded. Intra-human and inter-species aminoacid variability data estimated on the 13 coding for proteins genes of the 1255 human genomes and 60 mammalian species are also available. HmtDB is freely available, upon registration, at http://www.hmdb.uniba.it. CONCLUSION: The HmtDB project will contribute towards completing and/or refining haplogroup classification and revealing the real pathogenic potential of mitochondrial mutations, on the basis of variability estimation.

Computational Biology↗

PubMed2004

The evolution of the adenine nucleotide translocase family.

Homologous genes are grouped into families whose evolution may be different in the various organisms. For the variety of the processes and the well-known mechanism of gene gain and gene loss, which takes place in genome evolution, we deal in comparative analyses with a "one-to-many" or a "many-to-many" relationship between homologous genes going from invertebrates to vertebrates. In this scenario, it is important to understand how gene function has been preserved and in addition the innovations originated in a given lineage or species. The phylogenetic relations between gene family members and their molecular clock behavior may be very helpful to elucidate their functional fates in various organisms. This in turn can direct laboratory experiments and practical applications. In order to track the evolutionary history of the ANT gene family, we have collected and analyzed 46 sequences from fungi to mammals. Phylogenetic analyses have been performed on nucleotide and amino acidic sequences which have produced basically the same results. We observe the presence of multiple isoforms both in lower and higher eukaryotic species, thus a "many-to-many" correspondence between genes. The molecular phylogeny of ANT genes, reported in the present study, allows to date the time of divergence of ANT isoforms in various lineages. Furthermore, the logo analysis has been carried out to characterize the conservation features of ANT proteins particularly in their three similar domains originated by duplication.

Amino Acid Sequence↗

PubMed2004

Comparative genomics: the evolutionary history of the Bcl-2 family.

The Bcl-2 family is a huge family composed of various members, occurring in all animals, which are key regulators of apoptosis, the cell death program critical for cell survival and development, tissue homeostasis, and protection against pathogens. The members of the Bcl-2 family can be divided into pro-apoptotic and anti-apoptotic proteins. A delicate balance between these members exists in each cell and the regulations of these two groups of proteins determines whether the cell survives or undergoes apoptosis. Bcl-2 family proteins are characterized by distinct domains. All members possess at least one of the four motifs known as Bcl-2 homology domains (BH1 to BH4). Most pro-survival members which can inhibit apoptosis facing a wide variety of cytotoxic insults, contain at least BH1 and BH2 domains; those most similar to Bcl-2 have all four BH domains. All the pro-apoptosis family members possess BH3 domain which is the central domain. For the first time, a global phylogenetic analysis of all Bcl-2 family members is presented here. We have analyzed the genes known so far that have a different composition of the functional domains BH1, BH2, BH3 and BH4. The analyses were performed both on complete sequences (124 sites analyzed) and on single domains. We present the results obtained using both approaches. We have also analyzed the amino acid profile and the degree of conservation of the BH3 domains of pro- and anti-apoptotic proteins. The results of our phylogenetic analyses show that a clear-cut clustering into pro- and anti-apoptotic products, reproducible with different evolutionary methods, could also be obtained by analyzing restricted areas such as the BH1 and BH2 domains. It is noteworthy that even when the analysis is performed only on the BH3 domain, we have two clear-cut clusters. The evolutionary analysis of gene family members is a valuable tool to predict their functions and guide experimental assays to validate predictions. Once the functions of all the components are known, it will be possible to study the process in a holistic way.

Amino Acid Sequence↗

PubMed2004

Main features on tailed phage, host recognition and DNA uptake.

Phage nucleic acid transport is atypical among membrane transport and thus poses a fascinating problem: transport is unidirectional; it concerns a unique molecule the size of which may represent 50 times that of the bacterium. The rate of DNA transport can reach values as high as 3 to 4 thousands base pairs/sec. This raises many questions, which will be addressed in this review. Is there a single mechanism of transport for all types of phages? How does the phage genome overcome the hydrophobic barrier of the host envelope? Is DNA transported as a free molecule or in association with proteins? Is such transport dependent on phage and/or host cell components? What is the driving force for transport? Data will be presented for a few selected tailed phages, which are the most common type of phages and for which DNA transport has been most extensively studied. Part of the review is devoted to recent in vitro data which have allowed to partly decipher the mechanism of phage T5 DNA transport.

Biological Transport↗

PubMed2002

MitoNuc: a database of nuclear genes coding for mitochondrial proteins. Update 2002.

Mitochondria, besides their central role in energy metabolism, have recently been found to be involved in a number of basic processes of cell life and to contribute to the pathogenesis of many degenerative diseases. All functions of mitochondria depend on the interaction of nuclear and organelle genomes. Mitochondrial genomes have been extensively sequenced and analysed and data have been collected in several specialised databases. In order to collect information on nuclear coded mitochondrial proteins we developed MitoNuc, a database containing detailed information on sequenced nuclear genes coding for mitochondrial proteins in Metazoa. The MitoNuc database can be retrieved through SRS and is available via the web site http://bighost.area.ba.cnr.it/mitochondriome where other mitochondrial databases developed by our group, the complete list of the sequenced mitochondrial genomes, links to other mitochondrial sites and related information, are available. The MitoAln database, related to MitoNuc in the previous release, reporting the multiple alignments of the relevant homologous protein coding regions, is no longer supported in the present release. In order to keep the links among entries in MitoNuc from homologous proteins, a new field in the database has been defined: the cluster identifier, an alpha numeric code used to identify each cluster of homologous proteins. A comment field derived from the corresponding SWISS-PROT entry has been introduced; this reports clinical data related to dysfunction of the protein. The logic scheme of MitoNuc database has been implemented in the ORACLE DBMS. This will allow the end-users to retrieve data through a friendly interface that will be soon implemented.

Animals↗