Quantum classical simulations of the retinal chromophore photoisomerization event in newly discovered rhodopsins

The research presented and discussed in this thesis aims to enhance our understanding of how the spectroscopy and photochemical reactivity of conjugated double-bonds can be controlled at the supramolecular level (i.e. by incorporating the substrate in a specific macromolecular environment). This is achieved through the study of two recently discovered natural light-responsive proteins within the rhodopsin family. In fact, rhodopsins, together with phytochromes and xanthopsins, utilize an "elementary" light-induced double-bond isomerization reaction to catch, store, and subsequently leverage, the energy of light to trigger a multitude of biological functions across all the kingdoms of life. The research objective is, therefore, the mechanistic investigation of the photoisomerization taking place inside two different protein environments. This objective represents a meaningful goal for two main reasons. Firstly, it could provide novel insights into how nature exploits photoisomerization to incorporate light-sensitivity in proteins. Secondly, it could serve as a source of inspiration for bio-inspired technological applications, as the ability, invariably linked to this reaction, of these proteins to sense and respond to light has broad applications in various technological fields, such as optogenetics or synthetic biology. More specifically, this thesis reports on the computational investigation of two rhodopsins called Neorhodopsin (NeoR) and thermoplasmatales archaeon rhodopsin (TaHeR). NeoR was discovered in 2020 in the fungi spores produced by certain members of the phylum chytridiomycota and exhibits a set of extreme spectral properties that are particularly desirable in optogenetic tools. On the other hand, TaHeR is a rhodopsin expressed in the archea thermoplasmatales archaeon and belongs to the novel and elusive heliorhodopsin (HeR) family, only discovered in 2018. For both proteins, an in silico study of the photoisomerization event was carried out through the construction of two analogous hybrid quantum mechanics / molecular mechanics (QM/MM) models

Site-specific integration in mammalian cells mediated by a new hybrid baculovirus-adeno-associated virus vector

Baculovirus can transiently transduce primary human and rat hepatocytes, as well as a subset of stable celllines. To prolong transgene expression, we have developed new hybrid vectors which associate key elementsfrom adeno-associated virus (AAV) with the elevated transducing capacity of baculovirus. The hybrid vectorscontain a transgene cassette composed of the !-galactosidase (!-Gal) reporter gene and the hygromycin resistance(Hygr) gene flanked by the AAV inverted terminal repeats (ITRs), which are necessary for AAV replicationand integration in the host genome. Constructs were derived both with and without the AAV rep geneunder the p5 and p19 promoters cloned in different positions with respect to the baculovirus polyheidrinpromoter. A high-titer preparation of baculovirus-AAV (Bac-AAV) chimeric virus containing the ITR–Hygr–!-Gal sequence was obtained with insect cells only when the rep gene was placed in an antisense orientationto the polyheidrin promoter. Infection of 293 cells with Bac-AAV virus expressing the rep gene results in a 10-to 50-fold increase in the number of Hygr stable cell clones. Additionally, rep expression determined the localizationof the transgene cassette in the aavs1 site in approximately 41% of cases as detected by bothSouthern blotting and fluorescent in situ hybridization analysis. Moreover, site-specific integration of the ITRflankedDNA was also detected by PCR amplification of the ITR-aavs1 junction in transduced human fibroblasts.These data indicate that Bac-AAV hybrid vectors can allow permanent, nontoxic gene delivery of DNAconstructs for ex vivo treatment of primary human cells

Retinal chromophore charge delocalization and confinement explain the extreme photophysics of Neorhodopsin

The understanding of how the rhodopsin sequence can be modified to exactly modulate the spectroscopic properties of its retinal chromophore, is a prerequisite for the rational design of more effective optogenetic tools. One key problem is that of establishing the rules to be satisfied for achieving highly fluorescent rhodopsins with a near infrared absorption. In the present paper we use multi-configurational quantum chemistry to construct a computer model of a recently discovered natural rhodopsin, Neorhodopsin, displaying exactly such properties. We show that the model, that successfully replicates the relevant experimental observables, unveils a geometrical and electronic structure of the chromophore featuring a highly diffuse charge distribution along its conjugated chain. The same model reveals that a charge confinement process occurring along the chromophore excited state isomerization coordinate, is the primary cause of the observed fluorescence enhancement

Updated Italian Tetrapod Ichnology Reference List

We provide a list of contribution by Italian scientists to tetrapod ichnology with papers on both material from Italy and abroad. Foreign author’s contributions on tetrapod ichnology based on material from Italy are also considered. The list updates the previous one published by D’Orazi Porchetti et al. (2008) and, as a result, includes works from 1869 up to now. Following the previous reference list, papers of non-Italian researchers on foreign material are reported when the material was found on Italian territory at the time of publication

A novel imaging marker of cortical “cellularity” in multiple sclerosis patients

Pathological data showed focal inflammation and regions of diffuse neuronal loss in the cortex of people with multiple sclerosis (MS). In this work, we applied a novel model (“soma and neurite density imaging (SANDI)”) to multishell diffusion-weighted MRI data acquired in healthy subjects and people with multiple sclerosis (pwMS), in order to investigate inflammation and degeneration-related changes in the cortical tissue of pwMS. We aimed to (i) establish whether SANDI is applicable in vivo clinical data; (ii) investigate inflammatory and degenerative changes using SANDI soma fraction (fsoma)—a marker of cellularity—in both cortical lesions and in the normal-appearing-cortex and (iii) correlate SANDI fsoma with clinical and biological measures in pwMS. We applied a simplified version of SANDI to a clinical scanners. We then provided evidence that pwMS exhibited an overall decrease in cortical SANDI fsoma compared to healthy subjects, suggesting global degenerative processes compatible with neuronal loss. On the other hand, we have found that progressive pwMS showed a higher SANDI fsoma in the outer part of the cortex compared to relapsing–remitting pwMS, possibly supporting current pathological knowledge of increased innate inflammatory cells in these regions. A similar finding was obtained in subpial lesions in relapsing–remitting patients, reflecting existing pathological data in these lesion types. A significant correlation was found between SANDI fsoma and serum neurofilament light chain—a biomarker of inflammatory axonal damage—suggesting a relationship between SANDI soma fraction and inflammatory processes in pwMS again. Overall, our data show that SANDI fsoma is a promising biomarker to monitor changes in cellularity compatible with neurodegeneration and neuroinflammation in the cortex of MS patients

Measurement of ISR-FSR interference in the processes e+ e- --> mu+ mu- gamma and e+ e- --> pi+ pi- gamma

Charge asymmetry in processes e+ e- --> mu+ mu- gamma and e+ e- --> pi+ pi- gamma is measured using 232 fb-1 of data collected with the BABAR detector at center-of-mass energies near 10.58 GeV. An observable is introduced and shown to be very robust against detector asymmetries while keeping a large sensitivity to the physical charge asymmetry that results from the interference between initial and final state radiation. The asymmetry is determined as afunction of the invariant mass of the final-state tracks from production threshold to a few GeV/c2. It is compared to the expectation from QED for e+ e- --> mu+ mu- gamma and from theoretical models for e+ e- --> pi+ pi- gamma. A clear interference pattern is observed in e+ e- --> pi+ pi- gamma, particularly in the vicinity of the f_2(1270) resonance. The inferred rate of lowest order FSR production is consistent with the QED expectation for e+ e- --> mu+ mu- gamma, and is negligibly small for e+ e- --> pi+ pi- gamma.Comment: 32 pages,29 figures, to be submitted to Phys. Rev.

Les droits disciplinaires des fonctions publiques : « unification », « harmonisation » ou « distanciation ». A propos de la loi du 26 avril 2016 relative à la déontologie et aux droits et obligations des fonctionnaires

The production of tt‾ , W+bb‾ and W+cc‾ is studied in the forward region of proton–proton collisions collected at a centre-of-mass energy of 8 TeV by the LHCb experiment, corresponding to an integrated luminosity of 1.98±0.02 fb−1 . The W bosons are reconstructed in the decays W→ℓν , where ℓ denotes muon or electron, while the b and c quarks are reconstructed as jets. All measured cross-sections are in agreement with next-to-leading-order Standard Model predictions.The production of $t\overline{t}$, $W+b\overline{b}$ and $W+c\overline{c}$ is studied in the forward region of proton-proton collisions collected at a centre-of-mass energy of 8 TeV by the LHCb experiment, corresponding to an integrated luminosity of 1.98 $\pm$ 0.02 \mbox{fb}^{-1}. The $W$ bosons are reconstructed in the decays $W\rightarrow\ell\nu$, where $\ell$ denotes muon or electron, while the $b$ and $c$ quarks are reconstructed as jets. All measured cross-sections are in agreement with next-to-leading-order Standard Model predictions

Study of the e(+)e(-) -> K+K- reaction in the energy range from 2.6 to 8.0 GeV

The $e^+e^-\to K^+K^-$ cross section and charged-kaon electromagnetic form factor are measured in the $e^+e^-$ center-of-mass energy range ($E$) from 2.6 to 8.0 GeV using the initial-state radiation technique with an undetected photon. The study is performed using 469 fb$^{-1}$ of data collected with the BABAR detector at the PEP-II $e^+e^-$ collider at center-of-mass energies near 10.6 GeV. The form factor is found to decrease with energy faster than $1/E^2$, and approaches the asymptotic QCD prediction. Production of the $K^+K^-$ final state through the $J/\psi$ and $\psi(2S)$ intermediate states is observed. The results for the kaon form factor are used together with data from other experiments to perform a model-independent determination of the relative phases between single-photon and strong amplitudes in $J/\psi$ and $\psi(2S)\to K^+K^-$ decays. The values of the branching fractions measured in the reaction $e^+e^- \to K^+K^-$ are shifted relative to their true values due to interference between resonant and nonresonant amplitudes. The values of these shifts are determined to be about $\pm5\%$ for the $J/\psi$ meson and $\pm15\%$ for the $\psi(2S)$ meson.Comment: 18 pages, 19 postscript figure

Observation of the B0 → ρ0ρ0 decay from an amplitude analysis of B0 → (π+π−)(π+π−) decays

Proton–proton collision data recorded in 2011 and 2012 by the LHCb experiment, corresponding to an integrated luminosity of 3.0 fb−1 , are analysed to search for the charmless B0→ρ0ρ0 decay. More than 600 B0→(π+π−)(π+π−) signal decays are selected and used to perform an amplitude analysis, under the assumption of no CP violation in the decay, from which the B0→ρ0ρ0 decay is observed for the first time with 7.1 standard deviations significance. The fraction of B0→ρ0ρ0 decays yielding a longitudinally polarised final state is measured to be fL=0.745−0.058+0.048(stat)±0.034(syst) . The B0→ρ0ρ0 branching fraction, using the B0→ϕK⁎(892)0 decay as reference, is also reported as B(B0→ρ0ρ0)=(0.94±0.17(stat)±0.09(syst)±0.06(BF))×10−6

Measurement of the (eta c)(1S) production cross-section in proton-proton collisions via the decay (eta c)(1S) -> p(p)over-bar

The production of the $\eta_c (1S)$ state in proton-proton collisions is probed via its decay to the $p \bar{p}$ final state with the LHCb detector, in the rapidity range $2.0 6.5$ GeV/c. The cross-section for prompt production of $\eta_c (1S)$ mesons relative to the prompt $J/\psi$ cross-section is measured, for the first time, to be $\sigma_{\eta_c (1S)}/\sigma_{J/\psi} = 1.74 \pm 0.29 \pm 0.28 \pm 0.18 _{B}$ at a centre-of-mass energy $\sqrt{s} = 7$ TeV using data corresponding to an integrated luminosity of 0.7 fb$^{-1}$, and $\sigma_{\eta_c (1S)}/\sigma_{J/\psi} = 1.60 \pm 0.29 \pm 0.25 \pm 0.17 _{B}$ at $\sqrt{s} = 8$ TeV using 2.0 fb$^{-1}$. The uncertainties quoted are, in order, statistical, systematic, and that on the ratio of branching fractions of the $\eta_c (1S)$ and $J/\psi$ decays to the $p \bar{p}$ final state. In addition, the inclusive branching fraction of $b$-hadron decays into $\eta_c (1S)$ mesons is measured, for the first time, to be $B ( b \rightarrow \eta_c X ) = (4.88 \pm 0.64 \pm 0.25 \pm 0.67 _{B}) \times 10^{-3}$, where the third uncertainty includes also the uncertainty on the $J/\psi$ inclusive branching fraction from $b$-hadron decays. The difference between the $J/\psi$ and $\eta_c (1S)$ meson masses is determined to be $114.7 \pm 1.5 \pm 0.1$ MeV/c$^2$.The production of the $\eta _c (1S)$ state in proton-proton collisions is probed via its decay to the $p\overline{p}$ final state with the LHCb detector, in the rapidity range $2.0 6.5 \mathrm{{\,GeV/}{ c}}$ . The cross-section for prompt production of $\eta _c (1S)$ mesons relative to the prompt ${{ J}}/{\psi }$ cross-section is measured, for the first time, to be $\sigma _{\eta _c (1S)}/\sigma _{{{{ J}}/{\psi }}} = 1.74\, \pm \,0.29\, \pm \, 0.28\, \pm \,0.18 _{{\mathcal{B}}}$ at a centre-of-mass energy ${\sqrt{s}} = 7 {~\mathrm{TeV}}$ using data corresponding to an integrated luminosity of 0.7 fb$^{-1}$ , and $\sigma _{\eta _c (1S)}/\sigma _{{{{ J}}/{\psi }}} = 1.60 \pm 0.29 \pm 0.25 \pm 0.17 _{{\mathcal{B}}}$ at ${\sqrt{s}} = 8 {~\mathrm{TeV}}$ using 2.0 fb$^{-1}$ . The uncertainties quoted are, in order, statistical, systematic, and that on the ratio of branching fractions of the $\eta _c (1S)$ and ${{ J}}/{\psi }$ decays to the $p\overline{p}$ final state. In addition, the inclusive branching fraction of ${b}$ -hadron decays into $\eta _c (1S)$ mesons is measured, for the first time, to be ${\mathcal{B}}( b {\rightarrow } \eta _c X ) = (4.88\, \pm \,0.64\, \pm \,0.29\, \pm \, 0.67 _{{\mathcal{B}}}) \times 10^{-3}$ , where the third uncertainty includes also the uncertainty on the ${{ J}}/{\psi }$ inclusive branching fraction from ${b}$ -hadron decays. The difference between the ${{ J}}/{\psi }$ and $\eta _c (1S)$ meson masses is determined to be $114.7 \pm 1.5 \pm 0.1 {\mathrm {\,MeV\!/}c^2}$ .The production of the $\eta_c (1S)$ state in proton-proton collisions is probed via its decay to the $p \bar{p}$ final state with the LHCb detector, in the rapidity range $2.0 6.5$ GeV/c. The cross-section for prompt production of $\eta_c (1S)$ mesons relative to the prompt $J/\psi$ cross-section is measured, for the first time, to be $\sigma_{\eta_c (1S)}/\sigma_{J/\psi} = 1.74 \pm 0.29 \pm 0.28 \pm 0.18 _{B}$ at a centre-of-mass energy $\sqrt{s} = 7$ TeV using data corresponding to an integrated luminosity of 0.7 fb$^{-1}$, and $\sigma_{\eta_c (1S)}/\sigma_{J/\psi} = 1.60 \pm 0.29 \pm 0.25 \pm 0.17 _{B}$ at $\sqrt{s} = 8$ TeV using 2.0 fb$^{-1}$. The uncertainties quoted are, in order, statistical, systematic, and that on the ratio of branching fractions of the $\eta_c (1S)$ and $J/\psi$ decays to the $p \bar{p}$ final state. In addition, the inclusive branching fraction of $b$-hadron decays into $\eta_c (1S)$ mesons is measured, for the first time, to be $B ( b \rightarrow \eta_c X ) = (4.88 \pm 0.64 \pm 0.29 \pm 0.67 _{B}) \times 10^{-3}$, where the third uncertainty includes also the uncertainty on the $J/\psi$ inclusive branching fraction from $b$-hadron decays. The difference between the $J/\psi$ and $\eta_c (1S)$ meson masses is determined to be $114.7 \pm 1.5 \pm 0.1$ MeV/c$^2$