State of the art in abdominal MRI structured reporting: a review

In the management of several abdominal disorders, magnetic resonance imaging (MRI) has the potential to significantly improve patient's outcome due to its diagnostic accuracy leading to more appropriate treatment choice. However, its clinical value heavily relies on the quality and quantity of diagnostic information that radiologists manage to convey through their reports. To solve issues such as ambiguity and lack of comprehensiveness that can occur with conventional narrative reports, the adoption of structured reporting has been proposed. Using a checklist and standardized lexicon, structured reports are designed to increase clarity while assuring that all key imaging findings related to a specific disorder are included. Unfortunately, structured reports have their limitations too, such as risk of undue report simplification and poor template plasticity. Their adoption is also far from widespread, and probably the ideal balance between radiologist autonomy and report consistency of has yet to be found. In this article, we aimed to provide an overview of structured reporting proposals for abdominal MRI and of works assessing its value in comparison to conventional free-text reporting. While for several abdominal disorders there are structured templates that have been endorsed by scientific societies and their adoption might be beneficial, stronger evidence confirming their imperativeness and added value in terms of clinical practice is needed, especially regarding the improvement of patient outcome

Beneficial Effects of Citrus Bergamia Polyphenolic Fraction on Saline Load-Induced Injury in Primary Cerebral Endothelial Cells from the Stroke-Prone Spontaneously Hypertensive Rat Model

High salt load is a known noxious stimulus for vascular cells and a risk factor for cardiovascular diseases in both animal models and humans. The stroke-prone spontaneously hypertensive rat (SHRSP) accelerates stroke predisposition upon high-salt dietary feeding. We previously demonstrated that high salt load causes severe injury in primary cerebral endothelial cells isolated from SHRSP. This cellular model offers a unique opportunity to test the impact of substances toward the mechanisms underlying high-salt-induced vascular damage. We tested the effects of a bergamot polyphenolic fraction (BPF) on high-salt-induced injury in SHRSP cerebral endothelial cells. Cells were exposed to 20 mM NaCl for 72 h either in the absence or the presence of BPF. As a result, we confirmed that high salt load increased cellular ROS level, reduced viability, impaired angiogenesis, and caused mitochondrial dysfunction with a significant increase in mitochondrial oxidative stress. The addition of BPF reduced oxidative stress, rescued cell viability and angiogenesis, and recovered mitochondrial function with a significant decrease in mitochondrial oxidative stress. In conclusion, BPF counteracts the key molecular mechanisms underlying high-salt-induced endothelial cell damage. This natural antioxidant substance may represent a valuable adjuvant to treat vascular disorders

Intrinsic Structural Features of the Human IRE1α Transmembrane Domain Sense Membrane Lipid Saturation

Activation of inositol-requiring enzyme (IRE1α) is an indispensable step in remedying the cellular stress associated with lipid perturbation in the endoplasmic reticulum (ER) membrane. IRE1α is a single-spanning ER transmembrane protein possessing both kinase and endonuclease functions, and its activation can be fully achieved through the dimerization and/or oligomerization process. How IRE1α senses membrane lipid saturation remains largely unresolved. Using both computational and experimental tools, we systematically investigated the dimerization process of the transmembrane domain (TMD) of IRE1α and found that, with help of the serine 450 residue, the conserved tryptophan 457 residue buttresses the core dimerization interface of IRE1α-TMD. BiFC (bimolecular fluorescence complementation) experiments revealed that mutation on these residues abolished the saturated fatty acid-induced dimerization in the ER membrane and subsequently inactivated IRE1α activity in vivo. Therefore, our results suggest that the structural elements of IRE1α-TMD serve as a key sensor that detects membrane aberrancy

HDV can constrain HBV genetic evolution in hbsag: Implications for the identification of innovative pharmacological targets

Chronic HBV + HDV infection is associated with greater risk of liver fibrosis, earlier hepatic decompensation, and liver cirrhosis hepatocellular carcinoma compared to HBV mono-infection. However, to-date no direct anti-HDV drugs are available in clinical practice. Here, we identified conserved and variable regions in HBsAg and HDAg domains in HBV + HDV infection, a critical finding for the design of innovative therapeutic agents. The extent of amino-acid variability was measured by Shannon-Entropy (Sn) in HBsAg genotype-D sequences from 31 HBV + HDV infected and 62 HBV mono-infected patients (comparable for demographics and virological-parameters), and in 47 HDAg genotype-1 sequences. Positions with Sn = 0 were defined as conserved. The percentage of conserved HBsAg-positions was significantly higher in HBV + HDV infection than HBV mono-infection (p = 0.001). Results were confirmed after stratification for HBeAg-status and patients’ age. A Sn = 0 at specific positions in the C-terminus HBsAg were correlated with higher HDV-RNA, suggesting that conservation of these positions can preserve HDV-fitness. Conversely, HDAg was characterized by a lower percentage of conserved-residues than HBsAg (p < 0.001), indicating higher functional plasticity. Furthermore, specific HDAg-mutations were significantly correlated with higher HDV-RNA, suggesting a role in conferring HDV replicative-advantage. Among HDAg-domains, only the virus-assembly signal exhibited a high genetic conservation (75% of conserved-residues). In conclusion, HDV can constrain HBsAg genetic evolution to preserve its fitness. The identification of conserved regions in HDAg poses the basis for designing innovative targets against HDV-infection

Structural and dynamical properties of central nervous system proteins with pharmaceutical and biotechnological potential.

Neurodegenerative diseases are widespread pathologies of large social impact that include: prion, Alzheimer and Parkinson disease, Huntington chorea and amyotrophic lateral sclerosis. The onset of such diseases is commonly associated with the accumulation of insoluble amyloid plaques in specific neuronal population. In this scenario, research activities for the prevention and the treatment of these diseases are focused on two distinct directions: (a) the enhancement of factors that promote the survival and maintenance of nerve cells and (b) the definition of the molecular processes that lead to onset of neurodegenerative diseases. In this framework, the main scopes of the present PhD project have been the analysis of structural/dynamic determinants of the function of neuroprotective proteins (neurotrophins) and the study of structural properties of amyloid aggregates and their toxic precursors. Neurotrophins (NTs) are homodimeric proteins that play a key role in the differentiation, survival and maintenance of nerve cells. This class of proteins include: nerve growth factor (NGF), Brain-Derived Factor (BDNF), neurotrophin 3 (NT3), neurotrophin 4 (NT4), and neurotrophin 6 (NT6). NTs act by binding to two distinct classes of transmembrane receptors. One is the p75NTR neurotrophin receptor and the other is the Trk family of tyrosine kinase receptors, which includes TrkA, TrkB, and TrkC. All mature NTs bind to p75NTR, but Trks are more selective. NGF interacts selectively with TrkA receptors, NT4 and BDNF selectively with TrkB receptors, and NT3 interacts with TrkC receptors. During the PhD, a detailed investigation of the dynamical properties of different regions of NTs was carried out by molecular dynamics techniques. Initially, these studies were focussed on the intrinsic conformational preferences of N-terminal region of the NTs. These N-terminal regions are important for the recognition and the specificity of NT-Trk binding. Indeed, N-terminal region of NGF in complex with TrkA has an α-helical conformation, whereas the NT4 in complex with TrkB receptor is in 3/10 helix conformation. However, both N-terminal regions of the two NTs are absent in the crystallographic models of isolated dimers and in complex with the p75NTR receptor, revealing their flexibility in the absence of receptor and a conformational transitions in the interaction with the Trk receptor. Our calculations unveil that for NT4-Nter, and to a lesser extent for NGF-Nter, the conformation of the peptide that is prone to the Trk binding is already present among the states that are energetically accessible to the isolated peptide. This consideration has suggested feasible strategies for the design of effective NT agonist/antagonists. Indeed, variants of these peptides with an increased helical propensity will better mimic the NT functions. Successive simulations carried out on the main body of NGF have provided a detailed picture of mechanisms of interaction with the p75NTR receptor, whose stoichiometry of binding is controversial. These results provided important information on the correlated motions of distant region of the protein. Moreover, essential dynamics analyses clearly indicate that most of the motions of the protein are highly symmetrical. On the basis of results, it has been concluded that the binding of p75NTR to NGF induces a significant "induced-fit” from symmetric structures to asymmetric structures. In the last years, enormous efforts have been made to obtain insights into the structure of the amyloid-like forms of proteins and peptides involved in the insurgence of neurodegenerative diseases. A characterization of the structure and dynamic properties of these aggregates is required to define the molecular mechanisms underlying these diseases for the development of effective therapeutic strategies. In addition, the considerable resistance of amyloid-like fibrils, combined with their flexibility, versatility and ability to self-assemble has stimulated a growing interest in the potential of these fibers in biotechnological fields as nanobiomaterials. Previous MD simulations have shown that some steric zipper models are endowed with a remarkable stability also in a crystal-free context. However, MD simulations were limited to peptides with polar and/or aromatic dry interfaces. In this scenario, a section of my PhD project was focused on MD simulations of various amyloidogenic structures recently determined. Primarily, were carried out MD studies of steric zipper assemblies whose dry interface involves exclusively aliphatic residues. These simulations have highlighted the key role of residues involved in the steric zipper interface. Indeed, aliphatic residues are not able to form the intra-sheet and inter-sheet interactions formed by polar and aromatic residues that likely provide a strong contribution to the steric zipper motif stability. Along this line, amyoid-like assemblies endowed with hydrophobic residues presumably require larger interfaces, as it is shown by the stability of MD simulation of HET-s protein with a larger steric zippers interface. Very recent crystallographic studies have shown that the same amyloidogenic peptide can adopt distinct steric zipper assemblies (polymorphs). Intriguingly, it has been postulated that the different polymorphs of the same polypeptide sequence may be representative of distinct strains. In this framework, a detailed analysis of dynamical properties of two polymorphic structures formed by a segment of the islet amyloid polypeptide (IAPP) was carried out during the PhD. The analyses of the MD simulations show that the two IAPP distinct polymorphs are stable in a crystalline-free environment. This finding supports the hypothesis that the occurrence of strains in neurodegenerative diseases may be related to the possibility that a single peptide/protein chain may self-associate in alternative steric zipper-based assemblies. The last section of present thesis was dedicated to the studies of human prion protein (HPrP) properties. These studies were conducted in collaboration with the University of Cambridge. Independent crystallographic studies have shown the involvement of the β-sheet of the HPrP in intermolecular interactions that lead to the association of two different molecules HPrP in the crystalline state. These observations suggest that this association may be representative of the early stages of aggregation of HPrP. In this framework, during the PhD project detailed replica exchange molecular dynamics (REMD) studies on the intrinsic stability of HPrP β-structure were conducted. In particular, simulations were conducted on different β-strand combinations taken either from HPrP monomer or dimeric crystalline assemblies. The REMD simulations conducted on the isolated two stranded β-sheet of the protein monomer indicate that this structure is remarkably stable. The stability of larger aggregates formed by the juxtaposition of two of these sheets, as detected in the crystalline state, is very limited stability. Interestingly, additional simulations indicate that these aggregates are stabilized by mutations linked to the insurgence of pathological states. The observation that the two stranded β-sheet of the prion monomer are intrinsically stable hold important implications for prion polymerization process and for the design of synthetic peptides that potentially can inhibit the aggregation process of human prion protein