Statistical validation of the root-mean-square-distance, a measure of protein structural proximity

Despite its well-documented limitations, the root-mean-square-distance (rmsd) between pairs of equivalent atoms is routinely used to monitor the degree of similarity between two optimally superposed protein three-dimensional structures. A robust method for assessing the statistical significance of the difference between two rmsd values is presented here. It is based on the comparison of two protein structures through the correlation coefficient between equivalent inter-atomic distances and the subsequent application of the Fisher transformation that allows one to estimate the probability of identity between two correlation coefficient values. The relationship between the rmsd and Fisher correlation coefficient allows then to estimate the statistical significance of the difference between two rmsd values. Such a procedure is exemplified with the analysis of the possible classifications of the immunoglobulin-like domains of filamin and is compared to related estimations of structural similarity. The possibility to estimate the probability of the difference between two rmsd values can be used to optimize the protein structural classifications and comparisons, independent of the procedure used to derive the rmsds.     

Tobramycin Supplemented Small-Diameter Vascular Grafts for Local Antibiotic Delivery: A Preliminary Formulation Study

Peripheral artery occlusive disease is an emerging cardiovascular disease characterized by the blockage of blood vessels in the limbs and is associated with dysfunction, gangrene, amputation, and a high mortality risk. Possible treatments involve by-pass surgery using autologous vessel grafts, because of the lack of suitable synthetic small-diameter vascular prosthesis. One to five percent of patients experience vascular graft infection, with a high risk of haemorrhage, spreading of the infection, amputation and even death. In this work, an infection-proof vascular graft prototype was designed and manufactured by electrospinning 12.5% w/v poly-L-lactic-co-glycolic acid solution in 75% v/v dichloromethane, 23.8% v/v dimethylformamide and 1.2% v/v water, loaded with 0.2% w/w_PLGA. Polymer and tobramycin concentrations were selected after viscosity and surface tension and after HPLC-UV encapsulation efficiency (EE%) evaluation, respectively. The final drug-loaded prototype had an EE% of 95.58% ± 3.14%, with smooth fibres in the nanometer range and good porosity; graft wall thickness was 291 ± 20.82 μm and its internal diameter was 2.61 ± 0.05 mm. The graft’s antimicrobic activity evaluation through time-kill assays demonstrated a significant and strong antibacterial activity over 5 days against Staphylococcus aureus and Escherichia coli. An indirect cell viability assay on Normal Human Dermal Fibroblasts (NHDF) confirmed the cytocompatibility of the grafts.     

Sample treatment considerations in the analysis of organic colorants by surface-enhanced Raman scattering

The introduction of surface-enhanced Raman spectroscopy (SERS) in the field of cultural heritage has significantly improved the analysis of the organic dyes and their complexes that have been used as textile dyes and pigments in paintings and other polychrome works of art since antiquity. Over the last five years, a number of different procedures have been developed by various research groups. In this Article, we evaluate the effect of pretreating samples by exposing them to hydrofluoric acid (HF) vapor prior to SERS analysis, a step designed to hydrolyze the dye-metal complexes and increase analyte adsorption on the nanosized metallic support, thus enhancing the SERS signal. Materials studied include pure colorants, commercial lake pigments, and fibers from dyed textiles, as well as actual aged samples, such as microscopic fragments of lakes on paper and ancient pigments and glazes from several works of art, covering a wide range of time, from the second century B.C. to the early 20th century. In each case, SERS spectra obtained with or without HF hydrolysis were critically evaluated. The pretreatment with HF vapor resulted in faster analysis and increased sensitivity in most cases, with the exception of dyed silk fibers, where silk protein hydrolyzates were found to interfere with SERS analysis. As a final point, a two-step procedure including SERS on untreated and treated samples is proposed as a standard approach: by analyzing a sample first without hydrolysis, and then, following removal of the colloid, upon HF treatment, the best and most reliable results for a great number of dyes and substrates are assured.     

Reaction and phases from monoclinic zirconia and calcium aluminate cement at high temperatures

Solid state reaction using m-ZrO₂ and high alumina cement as starting materials was studied. Various compositions containing different proportions of calcium aluminate cement (5–50 mol% CaO in ZrO₂) were reaction sintered at 1300–1500 °C. Crystalline phase formation and densification of Ca stabilized ZrO₂ composites was investigated by X-ray diffraction analysis, density and shrinkage measurements. Scanning electron microscopy (SEM) combined with energy dispersive X-ray spectroscopy was used to examine the microstructure. The main crystalline phases formed are related to the expected with the equilibrium phase diagram of the ZrO₂–CaO–Al₂O₃ system. Stabilized c-ZrO₂ is formed with the composition of Ca_0.15Zr_0.85O_1.85. The sintering of the mixtures leads to porous composites materials. Textural properties were analyzed considering the initial composition and the present crystalline phases.     

Bovine colostrum: Changes in lipid constituents in the first 5 days after parturition

Despite the great interest paid to protein components in colostrum, fat also plays an important role in the supply of essential nutrients to provide energy, increase metabolism, and protect the newborn calf against microbial infections. This work aimed to elucidate levels of different fat components in colostrum, in particular fatty acid (FA), triglyceride (TG), cholesterol, and phospholipid contents. Colostrum samples from primiparous and multiparous (3–5 lactations) Holstein dams, fed the same ration indoors, were collected on the first 5 d after parturition, analyzed, and compared with milk samples from the same cows collected at 5 mo of lactation. Fat content during the first 5 d of milking did not vary. However, the proportion of short-chain saturated FA increased and that of long-chain FA decreased. The concentration of n-3 FA was higher on the first day of calving than on the other days, with clear differences in the number and type of n-3 FA. Conjugated linoleic isomers and trans FA slowly increased from d 1 to 5, reaching a maximum at 5 mo of lactation. Changes in the distribution profile of TG were observed as lactation progressed, with a shift from a prevalence of high-carbon-number TG (C48–50) on d 1 to a bimodal distribution (maxima at C38 and C50) on d 5, characteristic of mid-lactation milk. Cholesterol content was high in the first hours after calving and rapidly decreased within 48 h. Colostrum sampled on d 1 also had a high content of phospholipids. Phosphatidylethanolamine and sphingomyelin were, respectively, lower and higher in the first 5 d than in mid-lactation milk. The influence of lactation number on colostrum fat composition was also considered and significant results were obtained for all FA groups (except for polyunsaturated and n-6 FA) and TG content.     

Modeling food matrix effects on chemical reactivity: Challenges and perspectives

ABSTRACT

The same chemical reaction may be different in terms of its position of the equilibrium (i.e., thermodynamics) and its kinetics when studied in different foods. The diversity in the chemical composition of food and in its structural organization at macro-, meso-, and microscopic levels, that is, the food matrix, is responsible for this difference. In this viewpoint paper, the multiple, and interconnected ways the food matrix can affect chemical reactivity are summarized. Moreover, mechanistic and empirical approaches to explain and predict the effect of food matrix on chemical reactivity are described. Mechanistic models aim to quantify the effect of food matrix based on a detailed understanding of the chemical and physical phenomena occurring in food. Their applicability is limited at the moment to very simple food systems. Empirical modeling based on machine learning combined with data-mining techniques may represent an alternative, useful option to predict the effect of the food matrix on chemical reactivity and to identify chemical and physical properties to be further tested. In such a way the mechanistic understanding of the effect of the food matrix on chemical reactions can be improved.     

Nature and extent of the exposure to fibrous amphiboles in Biancavilla

An epidemiological and environmental study in the Biancavilla area (Sicily, Italy) was recently prompted by an impressively high incidence of malignant pleural mesothelioma. Epidemiology suggested an environmental contamination by amphibole fibres rather than risks related to a specific occupational activity. The aim of this study is to describe the diffusion of fibrous amphiboles in the area and identify their source. Fibrous amphiboles were found in the products from the local quarries, which had been used for years to build houses. After sampling all around Biancavilla, three sites were detected and they were characterized by an abundant presence of mineral fibres. Fibrous amphiboles were also recovered from building materials (mortar and plasters) and airborne particulates sampled in urban sites with high dust emissions due mainly to unpaved roads. Moreover, amphibole fibres were detected in the lung tissue of a woman who died of pleural mesothelioma. The results of this study suggest that the amphibole fibre diffusion in the Biancavilla environment lasted for many years and had been maximum during the sixties and the seventies with the uncontrolled development of the local building industry. Today, the environmental situation results to be changed following both the closing of the stone quarries and the urbanization works after 2001, above all the asphalting of dusty roads. Anyway sporadic mesothelioma cases have still to be expected in the next years.     

Early Osteogenic Marker Expression in hMSCs Cultured onto Acid Etching-Derived Micro- and Nanotopography 3D-Printed Titanium Surfaces

Polyetheretherketone (PEEK) titanium composite (PTC) is a novel interbody fusion device that combines a PEEK core with titanium alloy (Ti6Al4V) endplates. The present study aimed to investigate the in vitro biological reactivity of human bone-marrow-derived mesenchymal stem cells (hBM-MSCs) to micro- and nanotopographies produced by an acid-etching process on the surface of 3D-printed PTC endplates. Optical profilometer and scanning electron microscopy were used to assess the surface roughness and identify the nano-features of etched or unetched PTC endplates, respectively. The viability, morphology and the expression of specific osteogenic markers were examined after 7 days of culture in the seeded cells. Haralick texture analysis was carried out on the unseeded endplates to correlate surface texture features to the biological data. The acid-etching process modified the surface roughness of the 3D-printed PTC endplates, creating micro- and nano-scale structures that significantly contributed to sustaining the viability of hBM-MSCs and triggering the expression of early osteogenic markers, such as alkaline phosphatase activity and bone-ECM protein production. Finally, the topography of 3D-printed PTC endplates influenced Haralick’s features, which in turn correlated with the expression of two osteogenic markers, osteopontin and osteocalcin. Overall, these data demonstrate that the acid-etching process of PTC endplates created a favourable environment for osteogenic differentiation of hBM-MSCs and may potentially have clinical benefit.     

Bactericidal/Permeability-Increasing Protein Downregulates the Inflammatory Response in In Vivo Models of Arthritis

We investigated the effects of bactericidal/permeability-increasing protein (BPI) alone or in combination with hyaluronic acid (HA) in two animal models: collagen-induced arthritis (CIA) and crystal-induced inflammation. In CIA, mice were intraperitoneally injected with PBS, HA, or BPI plus or minus HA, twice a week for 2 months, and then euthanized to collect paw and blood. Arthritis was assessed in ankle joints by clinical and histological evaluation. Pathogenic crystals were intraperitoneally injected in mice plus or minus BPI, or with a composition of BPI and HA. After sacrifice, total and differential leukocyte counts were determined. Cytokine levels were measured in serum and peritoneal fluids. In CIA mice, BPI improved clinical and histological outcomes (histological scores ≥2-fold), and downregulated inflammatory mediators (47–93%). In crystal-induced inflammation, BPI reduced leukocyte infiltration (total count: ≥60%; polymorphonuclear cells: ≥36%) and inhibited cytokine production (35–74%). In both models, when mice were co-treated with BPI and HA, the improvement of all parameters was greater than that observed after administration of the two substances alone. Results show that BPI attenuates CIA and inflammation in mice, and this effect is enhanced by HA co-administration. Combined use of BPI and HA represents an interesting perspective for new potential treatments in arthritis.     

Highly Charged Ru(II) Polypyridyl Complexes as Photosensitizer Agents in Photodynamic Therapy of Epithelial Ovarian Cancer Cells

Ovarian cancer recurrence is frequent and associated with chemoresistance, leading to extremely poor prognosis. Herein, we explored the potential anti-cancer effect of a series of highly charged Ru(II)-polypyridyl complexes as photosensitizers in photodynamic therapy (PDT), which were able to efficiently sensitize the formation of singlet oxygen upon irradiation (Ru1²⁺ and Ru2²⁺) and to produce reactive oxygen species (ROS) in their corresponding dinuclear metal complexes with the Fenton active Cu(II) ion/s ([CuRu1]⁴⁺ and [Cu₂Ru2]⁶⁺). Their cytotoxic and anti-tumor effects were evaluated on human ovarian cancer A2780 cells both in the absence or presence of photoirradiation, respectively. All the compounds tested were well tolerated under dark conditions, whereas they switched to exert anti-tumor activity following photoirradiation. The specific effect was mediated by the onset of programed cell death, but only in the case of Ru1²⁺ and Ru2²⁺ was preceded by the loss of mitochondrial membrane potential soon after photoactivation and ROS production, thus supporting the occurrence of apoptosis via type II photochemical reactions. Thus, Ru(II)-polypyridyl-based photosensitizers represent challenging tools to be further investigated in the identification of new therapeutic approaches to overcome the innate chemoresistance to platinum derivatives of some ovarian epithelial cancers and to find innovative drugs for recurrent ovarian cancer.