Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1

The quantitative characterization of mutational landscapes is a task of outstanding importance in evolutionary and medical biology: It is, for example, of central importance for our understanding of the phenotypic effect of mutations related to disease and antibiotic drug resistance. Here we develop a novel inference scheme for mutational landscapes, which is based on the statistical analysis of large alignments of homologs of the protein of interest. Our method is able to capture epistatic couplings between residues, and therefore to assess the dependence of mutational effects on the sequence context where they appear. Compared with recent large-scale mutagenesis data of the beta-lactamase TEM-1, a protein providing resistance against beta-lactam antibiotics, our method leads to an increase of about 40% in explicative power as compared with approaches neglecting epistasis. We find that the informative sequence context extends to residues at native distances of about 20 Å from the mutated site, reaching thus far beyond residues in direct physical contact

Modelling the Microstructure and the Viscoelastic Behaviour of Carbon Black Filled Rubber Materials from 3D Simulations

Volume fraction and spatial repartition of fillers impact the physical properties of rubber. Extended percolating networks of nano-sized fillers significantly modify the macroscopic mechanical properties of rubbers. Random models that describe the multiscale microstructure of rubber and efficient Fourier-based numerical algorithms are combined to predict the material’s mechanical properties. From TEM image analysis, various types of multiscale models were proposed and validated, accounting for the non-homogeneous distribution of fillers: in the present work, aggregates are located outside of an exclusion polymer simulated by two families of random models. The first model generates the exclusion polymer by a Boolean model of spheres. In the second model, the exclusion polymer is a mosaic model built from a Johnson-Mehl tessellation. Here the exclusion polymer and the polymer containing the filler show a similar morphology, contrary to the Boolean model. Aggregates are then described as the intersection of a Boolean model of spheres and of the complementary of the exclusion polymer. Carbon black particles are simulated by a Cox model of spheres in the aggregates. The models rely on a limited number of parameters fitted from experimental covariance and cumulative granulometry. The influence of the model parameters on percolation properties of the models is studied numerically from 3D simulations. Finally, a novel Fourier-based algorithm is proposed to estimate the viscoelastic properties of linear heterogeneous media, in the harmonic regime. The method is compared to analytical results and to a different, time-discretized FFT scheme. As shown in this work, the proposed numerical method is efficient for computing the viscoelastic response of microstructures containing rubbers and fillers

Implant-Prosthetic rehabilitation in bilateral agenesis of maxillary lateral incisors with a mini split crest

The reported clinical case describes the surgical procedure of ridge augmentation by using a "split crest" technique with a partial thickness flap and a subsequent implant-prosthetic rehabilitation aimed at treating a bilateral agenesis of the upper lateral incisors. In such cases with vestibule-palatal and mesial-distal scarce bone thicknesses associated with the need of a proper functional and aesthetic rehabilitation, the split crest technique is particularly suitable. In the case we reported, because of the poor bone thicknesses, we performed a minimally invasive split crest which allowed a correct insertion of the fixtures. This technique allowed us to achieve an optimal functional and aesthetic rehabilitation; moreover, we obtained a good emergency profile, ensuring the vitality of the close teeth and ensuring a good primary stability and the following osseointegration of dental implants

Interleukin-6 stimulates gene expression of extracellular matrix components in bovine mesangial cells in culture

The effect of interleukin-6 (IL-6) on gene expression of extracellular matrix components in bovine mesangial cells in culture has been investigated. IL-6 (100 U/ml) time dependently increased the steady state expression of mRNAs coding for α1 collagen III and fibronectin, both transcripts being 1.5- and 2.5-fold higher than basal level at 24 and 48 h, respectively. In contrast, IL-6 stimulated laminin mRNA expression only after 48 h incubation (2.5-fold upon basal level). These results suggest that IL-6 could favour glomerular matrix accumulation thus contributing to the development of glomerulosclerosis

Real-life appraisal on blood pressure targets achievement in adult outpatients at high cardiovascular risk

Background and aim: Although hypertension guidelines highlight the benefits of achieving the recommended blood pressure (BP) targets, hypertension control rate is still insufficient, mostly in high or very high cardiovascular (CV) risk patients. Thus, we aimed to estimate BP control in a cohort of patients at high CV risk in both primary and secondary prevention. Methods and results: A single-center, cross-sectional study was conducted by extracting data from a medical database of adult outpatients aged 40–75 years, who were referred to our Hypertension Unit, Rome (IT), for hypertension assessment. Office BP treatment targets were defined according to 2018 ESC/ESH guidelines as: a)<130/80 mmHg in individuals aged 40–65 years; b)<140/80 mmHg in subjects aged >65 years. Primary prevention patients with SCORE <5% were considered to be at low-intermediate risk, whilst individuals with SCORE ≥5% or patients with comorbidities were defined to be at very high risk. Among 6354 patients (47.2% female, age 58.4 ± 9.6 years), 4164 (65.5%) were in primary prevention with low-intermediate CV risk, 1831 (28.8%) in primary prevention with high-very high CV risk and 359 (5.6%) in secondary prevention. In treated hypertensive outpatients, uncontrolled hypertension rate was significantly higher in high risk primary prevention than in low risk primary prevention and secondary prevention patients (18.4% vs 24.4% vs. 12.5%, respectively; P < 0.001). In high risk primary prevention diabetic patients only 10% achieved the recommended BP targets. Conclusions: Our data confirmed unsatisfactory BP control among high-risk patients, both in primary and secondary prevention, and suggest the need for a more stringent BP control policies in these patients

Two-photon polymerized "nichoid" substrates maintain function of pluripotent stem cells when expanded under feeder-free conditions

BACKGROUND: The use of pluripotent cells in stem cell therapy has major limitations, mainly related to the high costs and risks of exogenous conditioning and the use of feeder layers during cell expansion passages. METHODS: We developed an innovative three-dimensional culture substrate made of “nichoid” microstructures, nanoengineered via two-photon laser polymerization. The nichoids limit the dimension of the adhering embryoid bodies during expansion, by counteracting cell migration between adjacent units of the substrate by its microarchitecture. We expanded mouse embryonic stem cells on the nichoid for 2 weeks. We compared the expression of pluripotency and differentiation markers induced in cells with that induced by flat substrates and by a culture layer made of kidney-derived extracellular matrix. RESULTS: The nichoid was found to be the only substrate, among those tested, that maintained the expression of the OCT4 pluripotency marker switched on and, simultaneously, the expression of the differentiation markers GATA4 and α-SMA switched off. The nichoid promotes pluripotency maintenance of embryonic stem cells during expansion, in the absence of a feeder layer and exogenous conditioning factors, such as the leukocyte inhibitory factor. CONCLUSIONS: We hypothesized that the nichoid microstructures induce a genetic reprogramming of cells by controlling their cytoskeletal tension. Further studies are necessary to understand the exact mechanism by which the physical constraint provided by the nichoid architecture is responsible for cell reprogramming. The nichoid may help elucidate mechanisms of pluripotency maintenance, while potentially cutting the costs and risks of both feed-conditioning and exogenous conditioning for industrial-scale expansion of stem cells. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13287-016-0387-z) contains supplementary material, which is available to authorized users

How glassy are neural networks?

In this paper we continue our investigation on the high storage regime of a neural network with Gaussian patterns. Through an exact mapping between its partition function and one of a bipartite spin glass (whose parties consist of Ising and Gaussian spins respectively), we give a complete control of the whole annealed region. The strategy explored is based on an interpolation between the bipartite system and two independent spin glasses built respectively by dichotomic and Gaussian spins: Critical line, behavior of the principal thermodynamic observables and their fluctuations as well as overlap fluctuations are obtained and discussed. Then, we move further, extending such an equivalence beyond the critical line, to explore the broken ergodicity phase under the assumption of replica symmetry and we show that the quenched free energy of this (analogical) Hopfield model can be described as a linear combination of the two quenched spin-glass free energies even in the replica symmetric framework

Hybrid fibroin/polyurethane small-diameter vascular grafts: from fabrication to in vivo preliminary assessment

To address the need of alternatives to autologous vessels for small-calibre vascular applications (e.g. cardiac surgery), a bio-hybrid semi-degradable material composed of silk fibroin (SF) and polyurethane (Silkothane (R)) was herein used to fabricate very small-calibre grafts (o(in) = 1.5 mm) via electrospinning. Bio-hybrid grafts were in vitro characterized in terms of morphology and mechanical behaviour, and compared to similar grafts of pure SF. Similarly, two native vessels from a rodent model (abdominal aorta and vena cava) were harvested and characterized. Preliminary implants were performed on Lewis rats to confirm the suitability of Silkothane (R) grafts for small-calibre applications, specifically as aortic insertion and femoral shunt. The manufacturing process generated pliable grafts consisting of a randomized fibrous mesh and exhibiting similar geometrical features to rat aortas. Both Silkothane (R) and pure SF grafts showed radial compliances in the range from 1.37 +/- 0.86 to 1.88 +/- 1.01% 10(-2) mmHg(-1), lower than that of native vessels. The Silkothane (R) small-calibre devices were also implanted in rats demonstrating to be adequate for vascular applications; all the treated rats survived the surgery for three months after implantation, and 16 rats out of 17 (94%) still showed blood flow inside the graft at sacrifice. The obtained results lay the basis for a deeper investigation of the interaction between the Silkothane (R) graft and the implant site, which may deal with further analysis on the potentialities in terms of degradability and tissue formation, on longer time-points

Antisense Oligonucleotide: Basic Concepts and Therapeutic Application in Inflammatory Bowel Disease

Several molecular technologies aimed at regulating gene expression that have been recently developed as a strategy to combat inflammatory and neoplastic diseases. Among these, antisense technology is a specific, rapid, and potentially high-throughput approach for inhibiting gene expression through recognition of cellular RNAs. Advances in the understanding of the molecular mechanisms that drive tissue damage in different inflammatory diseases, including Crohn’s disease (CD) and ulcerative colitis (UC), the two major inflammatory bowel diseases (IBDs) in humans, have facilitated the identification of novel druggable targets and offered interesting therapeutic perspectives for the treatment of patients. This short review provides a comprehensive understanding of the basic concepts underlying the mechanism of action of the oligonucleotide therapeutics, and summarizes the available pre-clinical and clinical data for oligonucleotide-based therapy in IBD