Analysis of retroviral assembly and maturation using cryo-electron tomography

Retroviruses are a family of membrane-enveloped RNA viruses that can retrotranscribe and integrate their genome in the host cell chromatin. During the active production of virions the structural polyprotein Gag assembles together with the genomic RNA to form immature particles, which bud out from the host cell. After budding the Gag protein undergoes proteolytic maturation and is cleaved into MA, CA, NC, p6 and two spacer peptides, SP1 and SP2. This leads to dramatic changes in the core morphology and the gain of infectivity. The immature retro-virions are known to have Gag organized into a round, incomplete hexameric lattice with a spacing of ~7.5nm. The core of mature virions is organized into a mixture of hexamers and pentamers which are organized along a lattice with a spacing of ~9.6nm. The shape of the core in the mature virions is genus-dependent, but can be cylindrical, conical or round. During my PhD I have studied the immature Gag assembly across four retroviral genera in order to understand the structural requirements for the assembly of the immature retroviral lattice, and to shed more light on the principles of HIV-1 maturation. The major conclusions of my studies are the following: The CA region of Gag is the most structurally conserved across genera. The presence of a domain upstream of CA is not critical for the assembly although it stabilizes the lattice. In order to maintain an immature lattice is important to have a Gag multimerization domain downstream of CA. The region between CA and NC, which is highly variable, is not critical for the assembly but it can stabilise the lattice and therefore affect the structural changes that occur during the maturation. The maturation in retroviruses is an extremely fast process. In order to investigate the structural changes occurring during the maturation in HIV-1 I analysed the products of partial Gag maturation, which were obtained through selective mutations of the cleavage sites in Gag. This confirmed that the order in which Gag cleavages occur is important for a correct processing. The immature Gag lattice is destabilized only if both sides of the CA-SP1 region are cleaved. Furthermore, it showed that the condensation of the RNP has an effect on the core morphology in the mature virion

Analysis of the spatial and dynamical properties of a multiscale model of intestinal crypts

The preliminary analyses on a multiscale model of intestinal crypt dynamics are here presented. The model combines a morphological model, based on the Cellular Potts Model (CPM), and a gene regulatory network model, based on Noisy Random Boolean Networks (NRBNs). Simulations suggest that the stochastic differentiation process is itself sufficient to ensure the general homeostasis in the asymptotic states, as proven by several measures

Application of the Polynomial Chaos Expansion to the Uncertainty Propagation in Fault Transients in Nuclear Fusion Reactors: DTT TF Fast Current Discharge

Nuclear fusion reactors are composed of several complex components whose behavior may be not certain a priori. This uncertainty may have a significant impact on the evolution of fault transients in the machine, causing unexpected damage to its components. For this reason, a suitable method for the uncertainty propagation during those transients is required. The Monte Carlo method would be the reference option, but it is, in most of the cases, not applicable due to the large number of required, repeated simulations. In this context, the Polynomial Chaos Expansion has been considered as a valuable alternative. It allows us to create a surrogate model of the original one in terms of orthogonal polynomials. Then, the uncertainty quantification is performed repeatedly, relying on this much simpler and faster model. Using the fast current discharge in the Divertor Tokamak Test Toroidal Field (DTT TF) coils as a reference scenario, the following method has been applied: the uncertainty on the parameters of the Fast Discharge Unit (FDU) varistor disks is propagated to the simulated electrical and electromagnetic relevant effects. Eventually, two worst-case scenarios are analyzed from a thermal–hydraulic point of view with the 4C code, simulating a fast current discharge as a consequence of a coil quench. It has been demonstrated that the uncertainty on the inputs (varistor parameters) strongly propagates, leading to a wide range of possible scenarios in the case of accidental transients. This result underlines the necessity of taking into account and propagating all possible uncertainties in the design of a fusion reactor according to the Best Estimate Plus Uncertainty approach. The uncertainty propagation from input data to electrical, electromagnetic, and thermal hydraulic results, using surrogate models, is the first of its kind in the field of the modeling of superconducting magnets for nuclear fusion applications

Is social capital associated with synchronization in human communication? An analysis of Italian call records and measures of civic engagement

Social capital has been studied in economics, sociology and political science as one of the key elements that promote the development of modern societies. It can be defined as the source of capital that facilitates cooperation through shared social norms. In this work, we investigate whether and to what extent synchronization aspects of mobile communication patterns are associated with social capital metrics. Interestingly, our results show that our synchronization-based approach well correlates with existing social capital metrics (i.e., Referendum turnout, Blood donations, and Association density), being also able to characterize the different role played by high synchronization within a close proximity-based community and high synchronization among different communities. Hence, the proposed approach can provide timely, effective analysis at a limited cost over a large territory

Recent advances in retroviruses via cryo-electron microscopy

 Cryo-electron microscopy has undergone a revolution in recent years and it has contributed significantly to a number of different areas in biological research. In this manuscript, we will describe some of the recent advancements in cryo-electron microscopy focussing on the advantages that this technique can bring rather than on the technology. We will then conclude discussing how the field of retrovirology has benefited from cryo-electron microscopy

Juno: a Python-based graphical package for optical system design

This report introduces Juno, a modular Python package for optical design and simulation. Juno consists of a complete library that includes a graphical user interface to design and visualise arbitrary optical elements, set up wave propagation simulations and visualise their results. To ensure an efficient visualisation of the results, all simulation data are stored in a structured database that can filter and sort the output. Finally, we present a practical use case for Juno, where optical design and fabrication are interlaced in a feedback cycle. The presented data show how to compare the simulated and the measured propagation; if a difference or unexpected behaviour is found, we show how to convert and import the optical element profile from a profilometer measurement. The propagation through the profile can provide immediate feedback about the quality of the element and a measure of the effects brought by differences between the idealised and the actual profile, therefore, allowing to exclude the experimental errors and to weigh every aspect of fabrication errors.Comment: The software is available at https://github.com/DeMarcoLab/jun

Intragenic transcriptional cis-activation of the human immunodeficiency virus 1 does not result in allele-specific inhibition of the endogenous gene

<p>Abstract</p> <p>Background</p> <p>The human immunodeficiency virus type 1 (HIV-1) favors integration in active genes of host chromatin. It is believed that transcriptional interference of the viral promoter over the endogenous gene or vice versa might occur with implications in HIV-1 post-integrative transcriptional latency.</p> <p>Results</p> <p>In this work a cell line has been transduced with a HIV-based vector and selected for Tat-inducible expression. These cells were found to carry a single silent integration in sense orientation within the second intron of the <it>HMBOX1 </it>gene. The HIV-1 Tat transactivator induced the viral LTR and repressed <it>HMBOX1 </it>expression independently of vector integration. Instead, single-cell quantitative <it>in situ </it>hybridization revealed that allele-specific transcription of <it>HMBOX1 </it>carrying the integrated provirus was not affected by the transactivation of the viral LTR in <it>cis</it>.</p> <p>Conclusion</p> <p>A major observation of the work is that the HIV-1 genome has inserted in genes that are also repressed by Tat and this could be an advantage for the virus during transcriptional reactivation. In addition, it has also been observed that transcription of the provirus and of the endogenous gene in which it is integrated may coexist at the same time in the same genomic location.</p

Cyclic Plasticity and Low Cycle Fatigue of an AISI 316L Stainless Steel: Experimental Evaluation of Material Parameters for Durability Design

AISI 316L stainless steels are widely employed in applications where durability is crucial. For this reason, an accurate prediction of its behaviour is of paramount importance. In this work, the spotlight is on the cyclic response and low-cycle fatigue performance of this material, at room temperature. Particularly, the first aim of this work is to experimentally test this material and use the results as input to calibrate the parameters involved in a kinematic and isotropic nonlinear plasticity model (Chaboche and Voce). This procedure is conducted through a newly developed calibration procedure to minimise the parameter estimates errors. Experimental data are eventually used also to estimate the strain–life curve, namely the Manson–Coffin curve representing the 50% failure probability and, afterwards, the design strain–life curves (at 5% failure probability) obtained by four statistical methods (i.e., deterministic, “Equivalent Prediction Interval”, univariate tolerance interval, Owen’s tolerance interval for regression). Besides the characterisation of the AISI 316L stainless steel, the statistical methodology presented in this work appears to be an efficient tool for engineers dealing with durability problems as it allows one to select fatigue strength curves at various failure probabilities depending on the sought safety level