Paolo Calligari

Bio: Paolo Calligari is an academic researcher from University of Rome Tor Vergata. The author has contributed to research in topics: Allosteric regulation & Proto-oncogene tyrosine-protein kinase Src. The author has an hindex of 12, co-authored 31 publications receiving 491 citations. Previous affiliations of Paolo Calligari include International School for Advanced Studies & École Normale Supérieure.

Molecular Investigation of SARS-CoV-2 Proteins and Their Interactions with Antiviral Drugs.

Abstract: A new Coronavirus strain, named SARS-CoV-2, suddenly emerged in early December 2019. SARS-CoV-2 resulted in being dramatically infectious, with thousands of people infected. In this scenario, and without effective vaccines available, the importance of an immediate tool to support patients and against viral diffusion becomes evident. In this study, we exploit the molecular docking approach to analyze the affinity between different viral proteins and several inhibitors, originally developed for other viral infections. Our data show that, in some cases, a relevant binding can be detected. These findings support the hypothesis to develop new antiviral agents against COVID-19, on the basis of already established therapies.

Macrophage sensing of single-walled carbon nanotubes via Toll-like receptors.

Abstract: Carbon-based nanomaterials including carbon nanotubes (CNTs) have been shown to trigger inflammation. However, how these materials are 'sensed' by immune cells is not known. Here we compared the effects of two carbon-based nanomaterials, single-walled CNTs (SWCNTs) and graphene oxide (GO), on primary human monocyte-derived macrophages. Genome-wide transcriptomics assessment was performed at sub-cytotoxic doses. Pathway analysis of the microarray data revealed pronounced effects on chemokine-encoding genes in macrophages exposed to SWCNTs, but not in response to GO, and these results were validated by multiplex array-based cytokine and chemokine profiling. Conditioned medium from SWCNT-exposed cells acted as a chemoattractant for dendritic cells. Chemokine secretion was reduced upon inhibition of NF-κB, as predicted by upstream regulator analysis of the transcriptomics data, and Toll-like receptors (TLRs) and their adaptor molecule, MyD88 were shown to be important for CCL5 secretion. Moreover, a specific role for TLR2/4 was confirmed by using reporter cell lines. Computational studies to elucidate how SWCNTs may interact with TLR4 in the absence of a protein corona suggested that binding is guided mainly by hydrophobic interactions. Taken together, these results imply that CNTs may be 'sensed' as pathogens by immune cells.

Mutations in KCNK4 that Affect Gating Cause a Recognizable Neurodevelopmental Syndrome

Abstract: Aberrant activation or inhibition of potassium (K+) currents across the plasma membrane of cells has been causally linked to altered neurotransmission, cardiac arrhythmias, endocrine dysfunction, and (more rarely) perturbed developmental processes. The K+ channel subfamily K member 4 (KCNK4), also known as TRAAK (TWIK-related arachidonic acid-stimulated K+ channel), belongs to the mechano-gated ion channels of the TRAAK/TREK subfamily of two-pore-domain (K2P) K+ channels. While K2P channels are well known to contribute to the resting membrane potential and cellular excitability, their involvement in pathophysiological processes remains largely uncharacterized. We report that de novo missense mutations in KCNK4 cause a recognizable syndrome with a distinctive facial gestalt, for which we propose the acronym FHEIG (facial dysmorphism, hypertrichosis, epilepsy, intellectual disability/developmental delay, and gingival overgrowth). Patch-clamp analyses documented a significant gain of function of the identified KCNK4 channel mutants basally and impaired sensitivity to mechanical stimulation and arachidonic acid. Co-expression experiments indicated a dominant behavior of the disease-causing mutations. Molecular dynamics simulations consistently indicated that mutations favor sealing of the lateral intramembrane fenestration that has been proposed to negatively control K+ flow by allowing lipid access to the central cavity of the channel. Overall, our findings illustrate the pleiotropic effect of dysregulated KCNK4 function and provide support to the hypothesis of a gating mechanism based on the lateral fenestrations of K2P channels.

Nano-bio interactions: a neutrophil-centric view.

Abstract: Neutrophils are key components of the innate arm of the immune system and represent the frontline of host defense against intruding pathogens. However, neutrophils can also cause damage to the host. Nanomaterials are being developed for a multitude of different purposes and these minute materials may find their way into the body through deliberate or inadvertent exposure; understanding nanomaterial interactions with the immune system is therefore of critical importance. However, whereas numerous studies have focused on macrophages, less attention is devoted to nanomaterial interactions with neutrophils, the most abundant leukocytes in the blood. We discuss the impact of engineered nanomaterials on neutrophils and how neutrophils, in turn, may digest certain carbon-based materials such as carbon nanotubes and graphene oxide. We also discuss the role of the corona of proteins adsorbed onto the surface of nanomaterials and whether nanomaterials are sensed as pathogens by cells of the immune system.

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Abstract: : The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

The Noonan syndrome

Abstract: Two cases of Noonan syndrome are observed. The Noonan syndrome is a Turner-like syndrome with normal chromosomal constitution. Essential criteria in diagnosing the syndrome are the facial expression (hyper-telorisme, low-set and malformed ears, micrognathie, fish-like mouth). The short webbed neck and the cubitus valgus. These children are rather small and mental retardation can be present, especially in comparison with their siblings. Associated cardiac malformations occur in approximately 50% of the cases. We insist on audiologic findings. One case has a hearing impairment due to a malformation of the middle ear, recognised radiologically. The other has a deafness of perception type. Yet, the familial occurrence of last patient makes it doubtful whether this hearing loss can be linked to the Noonan-syndrome.

Signal analysis

Abstract: dix A. Even if you don’t choose to memorize them this system aids in reference and retreival of important formulas. The book was compiled from notes developed during eight years of teaching a graduate course on the subject and was used as a text. Thus it has been student tested. Appendix F contains a number of problems, grouped to be used on a chapter by chapter basis The problems are designed to illustrate practical applications of the text material. The parts of this book of most interest and value to the EMC engineer will be the chapters on Thermal Noise, Antennas, Propagation and Transmission Lines, and Reflection and Refraction. This is not to downpade the chapters on Statistics and Its Applications, Signal Processing and Detection, and Some System Characteristics which also contain much potentially useful materials. Additional plus values for the book include a list of 40 references, a table of symbols used throughout the book, and a subject index. Some readers may find the condensed type and close line spacing hard to read. It was apparently set up by typewriter using an elite type face with single line spacing. When reduced down to a 6 by 9 5 inch size page it is too crowded for easy reading. In spite of this shortcoming your reviewer recommends this book as a worthwhile reference in this field of interest.