Biomedical subjects

Alessandro Giuliani

Publications and source records attributed to Alessandro Giuliani.

At least 19 recordsLinked to original sources

PubMed2026

Integrative Multidimensional Profiling of Individuals Recovered from Mild COVID-19 Reveals Immune-Metabolic-Oxidative Network Interactions.

The COVID-19 pandemic underscored the need to better characterize immune and molecular responses following SARS-CoV-2 infection and vaccination. Beyond antibody and cellular immunity, COVID-19 involves oxidative stress and DNA damage, affecting repair mechanisms and metabolic adaptation linked to immune resilience. Here, we present a multidimensional analysis of 20 individuals who recovered from mild COVID-19, integrating clinical features with humoral and cellular immune responses, T cell and myeloid phenotypes, oxidative stress, DNA damage, and metabolomic and lipidomic profiles. Although most individual parameters fell within physiological ranges, network modeling revealed structured associations spanning multiple biological domains. A central finding was a coherent cluster organized around vaccine dose number, linking anti-Spike antibody titers, oxidative stress, bioenergetic signatures, and granulocyte activation. Higher vaccination was associated with stronger humoral responses, lower oxidative stress, and a more balanced myeloid-metabolic profile, suggesting a potential protective role extending beyond antibody induction. Additional associations linked symptom patterns to T cell differentiation states, anti-nucleocapsid responses to systemic inflammation, and anaerobic signatures to DNA damage markers, revealing interconnections between immunometabolism, clinical expression, and genomic stress. Despite the small sample size, these findings offer a preliminary systems-level perspective on mild COVID-19 recovery and illustrate the value of integrative exploratory frameworks in infectious disease research, laying the groundwork for validation in larger longitudinal cohorts.

Humans↗

PubMed2025

Structural obstruction to full DNA replication in terminally differentiated skeletal muscle cells.

Terminal cell differentiation is often associated with permanent withdrawal from proliferation, termed the postmitotic state. Though widespread among vertebrates and determinant for their biology, the molecular underpinnings of this state are poorly understood. Postmitotic skeletal muscle myotubes can be induced to reenter the cell cycle; however, they generally die as a result of their inability to complete DNA replication. Here, we explore the causes of such incompetence. Genomic hybridization of newly synthesized DNA shows that the replicative failure does not concern specific genomic regions, but can stochastically affect any of them. Myoblast and myotube nuclei are incubated in replicative Xenopus egg extract, which provides a full DNA replication machinery. While myoblast nuclei attain complete DNA replication, those from myotubes, even in these conditions, duplicate less than half of their genomes, strongly indicating that the structure of myotube chromatin obstructs DNA replication. Furthermore, disassembling and disorganizing chromatin with a strong salt treatment does not modify the replicative differences between the two types of nuclei, suggesting that they are rooted in the core structure of chromatin.

DNA Replication↗

PubMed2007

A topologically related singularity suggests a maximum preferred size for protein domains.

A variety of protein physicochemical as well as topological properties, demonstrate a scaling behavior relative to chain length. Many of the scalings can be modeled as a power law which is qualitatively similar across the examples. In this article, we suggest a rational explanation to these observations on the basis of both protein connectivity and hydrophobic constraints of residues compactness relative to surface volume. Unexpectedly, in an examination of these relationships, a singularity was shown to exist near 255-270 residues length, and may be associated with an upper limit for domain size. Evaluation of related G-factor data points to a wide range of conformational plasticity near this point. In addition to its theoretical importance, we show by an application of CASP experimental and predicted structures, that the scaling is a practical filter for protein structure prediction.

Binding Sites↗

PubMed2006

Dissecting drug and vehicle metabolic effects in rats by a metabonomic approach.

A combined application of high resolution (1)H NMR spectroscopy and multivariate statistical techniques focused on establishing a consistent statistical approach to metabonomic studies was tested. The data reduction, which is preliminary to the application of multivariate analysis to NMR spectra, was carried out by means of two complementary methods: pure Pattern Recognition (PR) and Assigned Signal Analysis (ASA). The simultaneous use of both approaches allowed us to obtain additional information in the analysis of metabonomic data, compared to the use of PR alone. This additional information consists in the possibility of a biochemical interpretation of the effects induced by treatment with xenobiotics, such as drugs or drug vehicles, on the metabolic networks of the systems under investigation. This approach allowed us to ascertain that a single-dose treatment with ST1959 vehicled by Sesame oil affects the production of hepatic glucose associated to an increment of the amino acid ketogenic process.

Algorithms↗

PubMed2006

Entropic criteria for protein folding derived from recurrences: six residues patch as the basic protein word.

Some research has suggested that patches of six constitute an important amino acid window length in proteins for conveying information. We present database evidence that supports this conjecture, as well as additional recurrence-based data that characterization and quantification of these words affect the folding/aggregation features of proteins. Other indirect evidence is presented and discussed.

Amino Acid Sequence↗

PubMed2006

Metabolic pathways variability and sequence/networks comparisons.

BACKGROUND: In this work a simple method for the computation of relative similarities between homologous metabolic network modules is presented. The method is similar to classical sequence alignment and allows for the generation of phenotypic trees amenable to be compared with correspondent sequence based trees. The procedure can be applied to both single metabolic modules and whole metabolic network data without the need of any specific assumption. RESULTS: We demonstrate both the ability of the proposed method to build reliable biological classification of a set of microorganisms and the strong correlation between the metabolic network wiring and involved enzymes sequence space. CONCLUSION: The method represents a valuable tool for the investigation of genotype/phenotype correlations allowing for a direct comparison of different species as for their metabolic machinery. In addition the detection of enzymes whose sequence space is maximally correlated with the metabolic network space gives an indication of the most crucial (on an evolutionary viewpoint) steps of the metabolic process.

Algorithms↗

PubMed2005

Functional essentiality from topology features in metabolic networks: a case study in yeast.

The relation between the position of mutations in Saccharomyces cerevisiae metabolic network and their lethality is the subject of this work. We represent the topology of the network by a directed graph: nodes are metabolites and arcs represent the reactions; a mutation corresponds to the removal of all the arcs referring to the deleted enzyme. Using publicly available knock-out data, we show that lethality corresponds to the lack of alternative paths in the perturbed network linking the nodes affected by the enzyme deletion. Such feature is at the basis of the recently recognized importance of 'marginal' arcs of metabolic networks.

Energy Metabolism↗

PubMed2005

Cognitive deficit associated with cholinergic and nerve growth factor down-regulation in experimental allergic encephalomyelitis in rats.

Clinical symptoms in multiple sclerosis include cognitive dysfunction. Difficulties in learning and remembering new information represent the most common cognitive deficit and are associated with a general and progressive brain pathology. Possible pathogenetic mechanisms for neuronal damage such as neuroprotective strategies are under active investigation also in experimental allergic encephalomyelitis, the most widely used experimental model for multiple sclerosis. In this paper we demonstrate that a selective deficit in learning and memory performance, as investigated by the Morris water maze test, is a consistent feature in rat encephalomyelitis, which correlates with a decline in choline acetyltransferase activity and nerve growth factor mRNA level in cerebral cortex, hippocampus, and basal forebrain. Treatment aimed to restore acetylcholine content through chronic administration of selective acetylcholinesterase inhibitors (rivastigmine and donepezil) restores cognitive performance, choline acetyltransferase activity, and nerve growth factor mRNA expression.

Animals↗

PubMed2005

Thyroid hormone and remyelination in adult central nervous system: a lesson from an inflammatory-demyelinating disease.

Re-myelination in the adult CNS has been demonstrated in different experimental models of demyelinating diseases. However, there is no clear evidence that re-myelination is effective in multiple sclerosis (MS), the most diffuse demyelinating disease. Moreover, chronic disabilities in MS are believed to be due to remyelination failure and consequent neuron damage and degeneration. Due to the presence of numerous oligodendrocyte precursors inside demyelination plaques, reasons for remyelination failure are unknown. In this paper, we reviewed data from embryonic development and in vitro studies supporting the primary role of thyroid hormone in oligodendrocyte maturation. We also reviewed personal data on the possibility of promoting myelination in chronic experimental allergic encephalomyelitis (EAE), a widely used experimental model of MS, by recruiting progenitors and channeling them into oligodendroglial lineage through the administration of thyroid hormone.

Animals↗

PubMed2005

Early events in protein aggregation: molecular flexibility and hydrophobicity/charge interaction in amyloid peptides as studied by molecular dynamics simulations.

In a previous article (Zbilut et al., Biophys J 2003;85:3544-3557), we demonstrated how an aggregation versus folding choice could be approached considering hydrophobicity distribution and charge. In this work, our aim is highlighting the mutual interaction of charge and hydrophobicity distribution in the aggregation process. Use was made of two different peptides, both derived from a transmembrane protein (amyloid precursor protein; APP), namely, Abeta(1-28) and Abeta(1-40). Abeta(1-28) has a much lower aggregation propensity than Abeta(1-40). The results obtained by means of molecular dynamics simulations show that, when submitted to the most "aggregation-prone" environment, corresponding to the isoelectric point and consequently to zero net charge, both peptides acquire their maximum flexibility, but Abeta(1-40) has a definitely higher conformational mobility than Abeta(1-28). The absence of a hydrophobic "tail," which is the most mobile part of the molecule in Abeta(1-40), is the element lacking in Abeta(1-28) for obtaining a "fully aggregating" phenotype. Our results suggest that conformational flexibility, determined by both hydrophobicity and charge effect, is the main mechanistic determinant of aggregation propensity.

Amyloid↗

PubMed2005

Randomized study on oral administration of calcitriol to prevent symptomatic hypocalcemia after total thyroidectomy.

BACKGROUND: Symptomatic hypocalcemia remains the main postoperative complication after total thyroidectomy. The aim of the present study was to evaluate the role of oral supplementation of calcitriol and calcium salts in preventing severe postoperative hypocalcemia after total thyroidectomy. METHODS: A consecutive series of patients undergoing total thyroidectomy followed by administration of 500 mg of calcium salts 3 times per day were randomized to 3 different postoperative medical treatments: in group A, .5 microg of calcitriol twice per day was administered to 104 patients; in group B, 1 mmicrog of calcitriol twice per day was administered to 111 patients; and in group C, 202 patients did not receive calcitriol. RESULTS: The rate of postoperative tetany in group A was 2.9%, in group B was 0%, and in group C was 7.4% (P=.03) and the rate of paresthesias was 28.8%, 17.1%, and 22.3%, respectively (P=.19). At discontinuation of calcitriol/calcium salts treatment, intact parathyroid hormone levels did not significantly differ from the preoperative levels. Receiver operating characteristic (ROC) curve analysis showed that the area under the curve for serum concentration of calcium in predicting postoperative tetany was .749, .858 and .862 on the first, second, and third postoperative day, respectively. The best cut-off value of calcemia for prediction tetany was 7.5 mg/dL, and the rate of severe hypocalcemia on the third postoperative day was 23.1% in group A, 9.9% in group B, and 27.2% in group C (P=.001). CONCLUSIONS: Oral administration of 1 microg of calcitriol twice per day and 500 mg of calcium salts 3 times per day after total thyroidectomy significantly decreases the risk of severe postoperative hypocalcemia.

Administration, Oral↗

PubMed2004

Thyroid hormone administration enhances remyelination in chronic demyelinating inflammatory disease.

Chronic disabilities in multiple sclerosis are believed to be due to neuron damage and degeneration, which follow remyelination failure. Due to the presence of numerous oligodendrocyte precursors inside demyelination plaques, one reason for demyelination failure could be the inability of oligodendrocyte precursor cells to turn into myelinating oligodendrocytes. In this study, we show that thyroid hormone enhances and accelerates remyelination in an experimental model of chronic demyelination, i.e., experimental allergic encephalomyelitis in congenic female Dark Agouti rats immunized with complete guinea pig spinal cord. Thyroid hormone, when administered during the acute phase of the disease, increases expression of platelet-derived growth factor alpha receptor, restores normal levels of myelin basic protein mRNA and protein, and allows an early and morphologically competent reassembly of myelin sheaths. Moreover, thyroid hormone exerts a neuroprotective effect with respect to axonal pathology.

Animals↗

PubMed2004

Discrimination of single amino acid mutations of the p53 protein by means of deterministic singularities of recurrence quantification analysis.

p53 is mutated in roughly 50% of all human tumors, predominantly in the DNA-binding domain codons. Structural, biochemical, and functional studies have reported that the different p53 mutants possess a broad range of behaviors that include the elimination of the tumor-suppression function of wild-type protein, the acquisition of dominant-negative function over the wild-type form, and the establishment of gain-of-function activities. The contribution of each of these types of mutations to tumor progression, grade of malignancy, and response to anticancer treatments has been so far analyzed only for a few "hot-spots." In an attempt to identify new approaches to systematically characterize the complete spectrum of p53 mutations, we applied recurrence quantification analysis (RQA), a non-linear signal analysis technique, to p53 primary structure. Moving from the study of the p53 hydrophobicity pattern, which revealed important similarities with the singular deterministic structuring of prions, we could statistically discriminate, on a pure amino acid sequence basis, between experimentally characterized DNA-contact defective and conformational p53 mutants with a very high percentage of success. This result indicates that RQA is a mathematical tool particularly advantageous for the development of a database of p53 mutations that integrates epidemiological data with structural and functional categorizations.

Amino Acid Sequence↗

PubMed2004

Stem cells and nervous tissue repair: from in vitro to in vivo.

Recent development in stem cell biology has indicated a new possible approach for the treatment of neurological diseases. However, in spite of tremendous hope generated, we are still on the way to understand if the use of stem cells to repair mature brain and spinal cord is a reliable possibility. In particular, we know very little on the in situ regulation of adult neural stem, and this also negatively impact on cell transplant possibilities. In this chapter we will discuss issues concerning the role and function of stem cells in neurological diseases, with regard to the impact of features of degenerating neurons and glial cells on in situ stem cells. Stem cell location and biology in the adult brain, brain host reaction to transplantation, neural stem cell reaction to experimental injuries and possibilities for exogenous regulation are the main topics discussed.

2',3'-Cyclic-Nucleotide Phosphodiesterases↗

PubMed2003

Otoacoustic emissions at different click intensities: invariant and subject-dependent features.

A study of click-evoked otoacoustic emissions (CEOAEs) elicited at stimulation intensities from 35 to >80 dB was carried out by recurrence quantification analysis on signals from both normal and hearing-impaired subjects. In normal subjects, a clear scaling of determinism with increasing stimulation intensity was observed in the click intensity range from 41 to 59 dB. Outside that range and, in particular, above its upper end, subject-dependent features appeared in the form of different maximal levels of determinism. A comparative analysis of responses from hearing-impaired subjects with conductive hearing losses and sensorineural hearing losses suggested that the principal contributor to this behavior is the middle ear and allowed us to discriminate the two pathologies solely on the basis of CEOAEs. These observations are consistent with a simple phenomenological model of the auditory periphery in which different functional modules are sequentially recruited at increasing stimulus intensities, with a consequent rise in CEOAE coherence.

Acoustic Stimulation↗

PubMed2003

Putting the Predictive Toxicology Challenge into perspective: reflections on the results.

MOTIVATION: Chemical carcinogenicity is of primary interest, because it drives much of the current regulatory actions regarding new and existing chemicals, and its experimental determination involves time-consuming and expensive animal testing. Both academia and private companies are actively trying to develop SAR and QSAR models. This paper reviews the new Predictive Toxicology Challenge (PTC) results, by putting them into the context of previous attempts. RESULTS: A marked dependency of the prediction ability of the different algorithms on the training sets was observed, pointing to a still insufficient coverage of the chemical carcinogens 'universe'. A theoretical treatment of the possible developments of the Artificial Intelligence approaches is sketched.

Algorithms↗

PubMed2003

Neural stem cells and cholinergic neurons: regulation by immunolesion and treatment with mitogens, retinoic acid, and nerve growth factor.

Degenerative diseases represent a severe problem because of the very limited repair capability of the nervous system. To test the potential of using stem cells in the adult central nervous system as "brain-marrow" for repair purposes, several issues need to be clarified. We are exploring the possibility of influencing, in vivo, proliferation, migration, and phenotype lineage of stem cells in the brain of adult animals with selective neural lesions by exogenous administration (alone or in combination) of hormones, cytokines, and neurotrophins. Lesion of the cholinergic system in the basal forebrain was induced in rats by the immunotoxin 192IgG-saporin. Alzet osmotic minipumps for chronic release (over a period of 14 days) of mitogens [epidermal growth factor (EGF) or basic fibroblast growth factor (bFGF)] were implanted in animals with behavioral and biochemical cholinergic defect and connected to an intracerebroventricular catheter. After 14 days of delivery, these pumps were replaced by others delivering nerve growth factor (NGF) for an additional 14 days. At the same time, retinoic acid was added to the rats' food pellets for one month. Whereas the lesion decreased proliferative activity, EGF and bFGF both increased the number of proliferating cells in the subventricular zone in lesioned and nonlesioned animals. These results are indicated by the widespread distribution of BrdUrd-positive nuclei in the forebrain, including in the cholinergic area. Performance in the water maze test was improved in these animals and choline acetyltransferase activity in the hippocampus was increased. These results suggest that pharmacological control of endogenous neural stem cells can provide an additional opportunity for brain repair. These studies also offer useful information for improving integration of transplanted cells into the mature brain.

Acetylcholine↗

PubMed2003

Large contact surface interactions between proteins detected by time series analysis methods: case study on C-phycocyanins.

A purely sequence-dependent approach to the modeling of protein-protein interaction was applied to the study of C-phycocyanin alphabeta dimers. The interacting pairs (alpha and beta subunits) share an almost complete structural homology, together with a general lack of sequence superposition; thus, they constitute a particularly relevant example for protein-protein interaction prediction. The present analysis is based on a description posited at an intermediate level between sequence and structure, that is, the hydrophobicity patterning along the chains. Based on the description of the sequence hydrophobicity patterns through a battery of nonlinear tools (recurrence quantification analysis and other sequence complexity descriptors), we were able to generate an explicit equation modeling alpha and beta monomers interaction; the model consisted of canonical correlation between the hydrophobicity autocorrelation structures of the interacting pairs. The general implications of this holistic approach to the modeling of protein-protein interactions, which considers the protein primary structures as a whole, are discussed.

Databases, Protein↗