Gene silencing and large-scale domain structure of the E. coli genome

The H-NS chromosome-organizing protein in E. coli can stabilize genomic DNA loops, and form oligomeric structures connected to repression of gene expression. Motivated by the link between chromosome organization, protein binding and gene expression, we analyzed publicly available genomic data sets of various origins, from genome-wide protein binding profiles to evolutionary information, exploring the connections between chromosomal organization, genesilencing, pseudo-gene localization and horizontal gene transfer. We report the existence of transcriptionally silent contiguous areas corresponding to large regions of H-NS protein binding along the genome, their position indicates a possible relationship with the known large-scale features of chromosome organization

Mining Biological Networks

This thesis addresses relevant issues related to the analysis of biological networks. Path redundancy was exploited to denoise currently available data, dominated by high levels of wrong or missing information, and applied to the local alignment of protein-protein interaction networks. On another research direction, regulatory networks were employed to explain master regulators’ ability of modulating cells’ behaviour. In this direction, an existing approach was adapted for the analysis of miRNAs’ role in Glioblastoma Multiforme cancer cells. The methodological aspects of this work represent an improvement of the foundamental elements of network analysis techniques

POLITICHE E ISTITUZIONI DEL SETTORE FORESTALE IN CINA

Il governo cinese da alcuni anni manifesta una politica a favore della protezione delle foreste naturali, dei divieti di taglio e di incentivo alla realizzazione di piantagioni arboree. La Repubblica Popolare è oggi il primo importatore di legname e il primo nella realizzazione di piantagioni con scopi produttivi e protettivi. Il presente elaborato vuole descrivere le politiche e le istituzioni del settore forestale in Cina, chiarire le modalità di gestione forestale, fornire una panoramica sul mercato dei prodotti forestali e sulla situazione delle piantagioni arboree del paese, in particolare analizzando i progetti forestali per lo sviluppo di quest’ultime. La Cina di oggi ha un urgente bisogno di legname. Nonostante sia il terzo stato al mondo per estensione del territorio, si presenta come un Paese povero di risorse forestali, con valori di stock pro capite nettamente inferiori alla media mondiale. Ciò è dovuto principalmente a quattro motivi: le caratteristiche climatiche, l’antropizzazione del territorio, le passate politiche di sfruttamento delle foreste naturali, il programma per la protezione delle foreste naturali. Per ovviare a questa carenza, oltre che per la proteggere il proprio territorio dal grave rischio di desertificazione e dalle alluvioni, il governo ha messo in atto i sei “programmi chiave” del settore forestale: il programma di protezione delle foreste naturali, il programma di conversione dei terreni agricoli in foresta, la “Grande Muraglia Verde” contro la desertificazione, il programma di protezione delle zone umide, il programma di controllo della desertificazione nei dintorni di Pechino e Tianjin, il programma di sviluppo delle piantagioni a crescita rapida e ad alta produttività. _______________________________________________________________________________________________________ From some years, the Chinese government expresses a policy for the protection and the prohibition of logging in natural forests and incentives for the creation of plantations of trees. People's Republic of China is now the largest importer of timber and the first country in the establishment of productive and protective plantations. The present study wants to describe the policies and institutions of the forestry sector in China, to clarify how forests are manages, to provide an overview of the forest products market and analyze the situation of trees plantations, notably by describing the reforestation projects. China has an urgent need for lumber. Despite being the third state in the world by extension, is presented as a poor country in forest resources, with values of stocks below comparing by the world average. This is mainly due for four reasons: the climate and land characteristics, the area of human activity, past policies of exploitation of natural forests, the program for the protection of natural forests. To remedy this deficiency, as well as for protecting its territory from the serious threat of desertification and floods, the government has implemented the “Six Key Forestry Programs": the Natural Forest Protection Program, the Program on Converting Cropland into Forest, the Shelterbelt Development Program, the Sandification Control Program near Beijing and Tianjin, the Wetlands Protection Program, the program on Fast-growing and High-yield Plantation. In addition to these, agro-forestry (mixture of trees plantations and agricultural crops, well developed in rural areas of the country), the forestry projects implemented by the Clean Development Mechanism, plantations for pulpwood financed by foreign companies and bamboo plantations contribute to a rapid increase in forest area in China. However, different issues are rising around the needing of timber in China (the largest growth in imports, the expansion of Chinese companies in the South East Asia countries) and the development of plantations (the loss of biodiversity due to the use of a few species, especially poplar, the use of genetically modified plants) shows that P.R.C. in need of further changes in forest sector, according of its economic development, its increasing population and the growing environmental problems.openTES-64

Interaction vs inhomogeneity in a periodic TASEP

We study the non-equilibrium steady states in a totally asymmetric simple exclusion process with periodic boundary conditions, also incorporating (i) an extra (nearest-neighbour) repulsive interaction and (ii) hopping rates characterized by a smooth spatial inhomogeneity. We make use of a generalized mean-field approach (at the level of nearest-neighbour pair clusters), in combination with kinetic Monte Carlo simulations. It turns out that the so-called shock phase can exhibit a lot of qualitatively different subphases, including multiple-shock phases, and a minimal-current shock phase. We argue that the resulting, considerably rich phase diagram should be relatively insensitive to minor details of either interaction or spatial inhomogeneity. As a consequence, we also expect that our results help elucidate the nature of shock subphases detected in previous studies

Serum Cystatin C for the diagnosis of acute Kidney Injury in Patients Admitted in the Emergency Department

BACKGROUND: Early diagnosis of acute kidney injury (AKI) at emergency department (ED) is a challenging issue. Current diagnostic criteria for AKI poorly recognize early renal dysfunction and may cause delayed diagnosis. We evaluated the use of serum cystatin C (CysC) for the early and accurate diagnosis of AKI in patients hospitalized from the ED. METHODS: In a total of 198 patients (105 males and 93 females), serum CysC, serum creatinine (sCr), and estimated glomerular filtration rate (eGFR) were calculated at 0, 6, 12, 24, 48, and 72 hours after presentation to the ED. We compared two groups according to the presence or absence of AKI. RESULTS: Serial assessment of CysC, sCr, and eGFR was not a strong, reliable tool to distinguish AKI from non-AKI. CysC > 1.44 mg/L at admission, both alone (Odds Ratio = 5.04; 95%CI 2.20-11.52; P < 0.0002) and in combination with sCr and eGFR (Odds Ratio = 5.71; 95%CI 1.86-17.55; P < 0.002), was a strong predictor for the risk of AKI. CONCLUSIONS: Serial assessment of CysC is not superior to sCr and eGFR in distinguishing AKI from non-AKI. Admission CysC, both alone and in combination with sCr and eGFR, could be considered a powerful tool for the prediction of AKI in ED patients

Comparison of Gingival Retraction Materials Using a New Gingival Sulcus Model

Purpose To investigate the pressure generated by different retraction materials using a novel gingival sulcus model. Materials and Methods A gingival sulcus model was made using a polymer frame filled with silicon. A pressure sensor and a sulcus‐fluid simulation were embedded into the silicon chamber to evaluate the pressure generated by different retraction materials. Six sizes of Ultrapak retraction cords (Ultradent, sizes #000 ‐ 3), 4 retraction pastes (Expazen, Expasyl, Acteon, Access Edge, Traxodent) and 2 retraction gels (Sulcus Blue, Racegel) were analyzed. The mean and median pressure, interquartile range, and standard deviation (SD) of n = 10 repeated measurements were calculated. Statistical analysis was conducted by Kruskal‐Wallis test for differences between the main groups of retraction materials, and Mann‐Whitney U‐test was performed to analyze differences between the single retraction materials. Results Pressure (mean ± SD) generated by retraction cords increased with increasing size (48.26 ± 11.29 kPa, size #000 to 149.27 ± 28.75 kPa for #3). There was a significant difference between sizes (p \u3c 0.01), except in #0 versus #1, and #2 versus #3. Retraction pastes generated pressures that ranged from 82.74 ± 29.29 kPa (Traxodent) to 524.35 ± 113.88 kPa (Expasyl). Retraction gels generated pressures from 38.96 ± 14.68 kPa (Racegel) to 95.15 ± 24.18 kPa (Sulcus Blue). Pressure generated by Expasyl was significantly higher than pressure generated by all other tested materials (p \u3c 0.001). Conclusion Pressure generated by retraction pastes and gels depends on the consistency of the retraction material, while pressure generated by retraction cords increased with increasing size of cords. Expasyl was found to generate the highest pressure compared to all other retraction materials

MISSEL: a method to identify a large number of small species-specific genomic subsequences and its application to viruses classification

Continuous improvements in next generation sequencing technologies led to ever-increasing collections of genomic sequences, which have not been easily characterized by biologists, and whose analysis requires huge computational effort. The classification of species emerged as one of the main applications of DNA analysis and has been addressed with several approaches, e.g., multiple alignments-, phylogenetic trees-, statistical- and character-based methods

Intermittency acceleration of water droplet population dynamics inside the interfacial layer between cloudy and clear air environments

We use direct numerical simulation to study the temporal evolution of a perturbation localized on the turbulent layer that typically separates a cloud from the surrounding clear air. Across this shearless layer, a turbulent kinetic energy gradient naturally forms. Here, a finite perturbation in the form of a local initial temperature fluctuation is applied to simulate a hydrodynamic instability inside the background turbulent air flow. A numerical initial value problem for two diametrically opposite types of drop population distributions is then solved. Specifically, we consider a mono-disperse population of droplets of 15 $\mu$m of radius and a poly-disperse distribution with radii in the range 0.6 - 30 $\mu$m. For both distributions, it is observed that the evaporation and condensation have a dramatically different weight inside the homogeneous cloudy region and the interfacial anisotropic mixing region. It is observed that the dynamics of drop collisions is highly effected by the turbulence structure of the host region. The two populations show a common aspect during their energy decay transient. That is the increased probability of collisions in the interfacial layer hat houses intense anisotropic velocity fluctuations. This layer, in fact, induces an enhanced differentiation on droplets kinetic energy and sizes. Both polydisperse and monodisperse initial particle distributions contain $10^7$ droplets, matching an initial liquid water content of $0.8 g/m^3$. An estimate of the turbulent collision kernel for geometric collisions used in the population balance equations is given. A preliminary discussion is presented on the structure of the two unsteady non ergodic collision kernels obtained inside the cloud interface region.Comment: Turbulent shearless layer, Cloud-clear air interaction, Inertial particles, Water droplets, DNS, Gravity effects, Collision kerne

Managing for the unexpected: Building resilient forest landscapes to cope with global change

Natural disturbances exacerbated by novel climate regimes are increasing worldwide, threatening the ability of forest ecosystems to mitigate global warming through car-bon sequestration and to provide other key ecosystem services. One way to cope with unknown disturbance events is to promote the ecological resilience of the forest by increasing both functional trait and structural diversity and by fostering functional connectivity of the landscape to ensure a rapid and efficient self- reorganization of the system. We investigated how expected and unexpected variations in climate and biotic disturbances affect ecological resilience and carbon storage in a forested region in southeastern Canada. Using a process- based forest landscape model (LANDIS-II), we simulated ecosystem responses to climate change and insect outbreaks under dif-ferent forest policy scenarios—including a novel approach based on functional diver-sification and network analysis—and tested how the potentially most damaging insect pests interact with changes in forest composition and structure due to changing cli-mate and management. We found that climate warming, lengthening the vegetation season, will increase forest productivity and carbon storage, but unexpected impacts of drought and insect outbreaks will drastically reduce such variables. Generalist, non- native insects feeding on hardwood are the most damaging biotic agents for our region, and their monitoring and early detection should be a priority for forest au-thorities. Higher forest diversity driven by climate-smart management and fostered by climate change that promotes warm-adapted species, might increase disturbance severity. However, alternative forest policy scenarios led to a higher functional and structural diversity as well as functional connectivity—and thus to higher ecological resilience—than conventional management. Our results demonstrate that adopting a landscape-scale perspective by planning interventions strategically in space and adopting a functional trait approach to diversify forests is promising for enhancing ecological resilience under unexpected global change stressors.MM received funding from the Swiss National Science Foundation (grant n.175101) and the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie framework (grant n.891671, REINFORCE project). NA was supported by a Juan de la Cierva fellowship of the Spanish Ministry of Science and Innovation (FCJ2020-046387-I). This work has also been supported by funding to NA and MM from the Canada Research Chair in Forest Resilience to Global Changes attributed to CM. MJF acknowledges the support of the Canada Research Chair in Spatial Ecology