Computational-Driven Epitope Verification and Affinity Maturation of TLR4-Targeting Antibodies

Toll-like receptor (TLR) signaling plays a critical role in the induction and progression of autoimmune diseases such as rheumatoid arthritis, systemic lupus erythematous, experimental autoimmune encephalitis, type 1 diabetes mellitus and neurodegenerative diseases. Deciphering antigen recognition by antibodies provides insights and defines the mechanism of action into the progression of immune responses. Multiple strategies, including phage display and hybridoma technologies, have been used to enhance the affinity of antibodies for their respective epitopes. Here, we investigate the TLR4 antibody-binding epitope by computational-driven approach. We demonstrate that three important residues, i.e., Y328, N329, and K349 of TLR4 antibody binding epitope identified upon in silico mutagenesis, affect not only the interaction and binding affinity of antibody but also influence the structural integrity of TLR4. Furthermore, we predict a novel epitope at the TLR4-MD2 interface which can be targeted and explored for therapeutic antibodies and small molecules. This technique provides an in-depth insight into antibody–antigen interactions at the resolution and will be beneficial for the development of new monoclonal antibodies. Computational techniques, if coupled with experimental methods, will shorten the duration of rational design and development of antibody therapeutics.     

Connexin 43 and Connexin 26 Involvement in the Ponatinib-Induced Cardiomyopathy: Sex-Related Differences in a Murine Model

Cardiac connexins (Cxs) are proteins responsible for proper heart function. They form gap junctions that mediate electrical and chemical signalling throughout the cardiac system, and thus enable a synchronized contraction. Connexins can also individually participate in many signal transduction pathways, interacting with intracellular proteins at various cellular compartments. Altered connexin expression and localization have been described in diseased myocardium and the aim of this study is to assess the involvement of Cx43, Cx26, and some related molecules in ponatinib-induced cardiac toxicity. Ponatinib is a new multi-tyrosine kinase inhibitor that has been successfully used against human malignancies, but its cardiotoxicity remains worrisome. Therefore, understanding its signaling mechanism is important to adopt potential anti cardiac damage strategies. Our experiments were performed on hearts from male and female mice treated with ponatinib and with ponatinib plus siRNA-Notch1 by using immunofluorescence, Western blotting, and proteomic analyses. The altered cardiac function and the change in Cxs expression observed in mice after ponatinib treatment, were results dependent on the Notch1 pathway and sex. Females showed a lower susceptibility to ponatinib than males. The downmodulation of cardiac Cx43, Cx26 and miR-122, high pS368-Cx43 phosphorylation, cell viability and survival activation could represent some of the female adaptative/compensatory reactions to ponatinib cardiotoxicity.     

Evaluation of Floxuridine Oligonucleotide Conjugates Carrying Potential Enhancers of Cellular Uptake

Conjugation of small molecules such as lipids or receptor ligands to anti-cancer drugs has been used to improve their pharmacological properties. In this work, we studied the biological effects of several small-molecule enhancers into a short oligonucleotide made of five floxuridine units. Specifically, we studied adding cholesterol, palmitic acid, polyethyleneglycol (PEG 1000), folic acid and triantennary N-acetylgalactosamine (GalNAc) as potential enhancers of cellular uptake. As expected, all these molecules increased the internalization efficiency with different degrees depending on the cell line. The conjugates showed antiproliferative activity due to their metabolic activation by nuclease degradation generating floxuridine monophosphate. The cytotoxicity and apoptosis assays showed an increase in the anti-cancer activity of the conjugates related to the floxuridine oligomer, but this effect did not correlate with the internalization results. Palmitic and folic acid conjugates provide the highest antiproliferative activity without having the highest internalization results. On the contrary, cholesterol oligomers that were the best-internalized oligomers had poor antiproliferative activity, even worse than the unmodified floxuridine oligomer. Especially relevant is the effect induced by palmitic and folic acid derivatives generating the most active drugs. These results are of special interest for delivering other therapeutic oligonucleotides.     

Direct-Ink-Writing of Electroactive Polymers for Sensing and Energy Storage Applications

Considering the high levels of materials used in the fields of electronics and energy storage systems, it is increasingly necessary to take into consideration environmental impact. Thus, it is important to develop devices based on environmentally friendlier materials and/or processes, such as additive manufacturing techniques. In this work, poly(vinylidene fluoride) (PVDF) and poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP) are prepared by direct-ink-writing (DIW) by varying solvent evaporation temperature and fill density percentage. Different morphologies for both polymers are obtained, including dense films and porous membranes, as well as different electroactive β-phase content, thermal and mechanical properties. The dielectric constant and piezoelectric d₃₃ coefficient for dense films reaches up to 16 at 1 kHz and 4 pC N⁻¹, respectively for PVDF-HFP with a fill density of 80 and a solvent evaporation temperature of 50 °C. Porous structures are developed for battery separator membranes in lithium-ion batteries, with a highest ionic conductivity value of 3.8 mS cm⁻¹ for the PVDF-HFP sample prepared with a fill density of 100 and a solvent evaporation temperature of 25 °C, the sample showing an excellent cycling performance. It is demonstrated that electroactive films and membranes can be prepared by direct-ink writing suitable for sensors/actuators and energy storage systems.     

Low-Thermal-Conductivity Rare-Earth Zirconates for Potential Thermal-Barrier-Coating Applications

Rare-earth zirconates have been identified as a class of low-thermal-conductivity ceramics for possible use in thermal barrier coatings (TBCs) for gas-turbine engine applications. To document and compare the thermal conductivities of important rare-earth zirconates, we have measured the thermal conductivities of the following hot-pressed ceramics: (i) Gd₂Zr₂O₇ (pyrochlore phase), (ii) Gd₂Zr₂O₇ (fluorite phase), (iii) Gd_2.58Zr_1.57O₇ (fluorite phase), (iv) Nd₂Zr₂O₇ (pyrochlore phase), and (v) Sm₂Zr₂O₇ (pyrochlore phase). We have also measured the thermal conductivity of pressureless-sintered 7 wt% yttria-stabilized zirconia (7YSZ)—the commonly used composition in current TBCs. All rare-earth zirconates investigated here showed nearly identical thermal conductivities, all of which were ∼30% lower than the thermal conductivity of 7YSZ in the temperature range 25°–700°C. This finding is discussed qualitatively with reference to thermal-conductivity theory.     

The Effects Of Humic Substances On Pinus Callus Are Reversed By 2,4-Dichlorophenoxyacetic Acid

The reversal of humic matter-induced inhibition of callus growth and metabolism by 2,4-dichlorophenoxyacetic acid (2,4-D) was studied in Pinus laricio. Two forest humic fractions (relative molecular mass (M_r) > 3500), derived from soil under Fagus sylvatica (Fs) and Abies alba (Aa) plantation, were used. Pinus laricio callus was grown for a subculture period (4 weeks) on Basal Murashige and Skoog (MS) medium plus forest humic matters (Fs or Aa), at a concentration of 1 mg C/l, and then was transferred, for an additional four weeks, to a MS medium culture without humic matter, but with different hormones: indole-3-acetic acid (IAA, 2 mg/1) or 2,4-dichlorophenoxyacetic acid (2,4-D, 0.5 mg/1) and/or 6-benzylaminopurine (BAP, 0.25 mg/1). Growth of calluse, glucose, fructose, and sucrose contents, and activities of soluble and bound invertases, glucokinase, phosphoglucose isomerase, aldolase, and pyruvate kinase were monitored. The results show a negative effect of humic fractions on callus growth, due to decreased utilization of glucose and fructose, and decreased activities of glycolytic enzymes. The effects are reversible. Substitution of humic fractions with 2,4-D+BAP or 2,4-D is followed by an increase of glycolytic enzyme activities and, consequently, by the utilization of glucose and fructose that induces a restart of growth. In contrast, the inhibitory effects of humic fractions persist when they are substituted with BAP alone, indicating that only the auxin 2,4-D is capable of reversing the negative effects. A possible competitive action on the auxin-binding site between 2,4-D and the chemical structures in the forest humic fractions is suggested.     

Learning control in spatial coordinates for the path-following of autonomous vehicles

We prove the existence of a P-type (proportional-type) space-learning control, which, on the basis of a kinematic third order nonlinear model of an autonomous nonholonomic vehicle and by a proper choice of the proportional control gain, guarantees asymptotic tracking of planar curves whose uncertain curvature is L$L$-periodic in the curvilinear abscissa. The behavior of a human driver, who repetitively learns the correct action from the past experience in the space, is mathematically reproduced. A stability analysis is presented while simulation results demonstrate the effectiveness of the presented approach.     

Ion‐exchange resins. II. Acrylamide crosslinked copolymers as precursors for some ion exchangers

Crosslinked copolymers of acrylamide (AA) and ethylacrylate and some ion exchangers derived from them containing either primary amine groups, obtained by the Hofmann degradation of the amide groups, or carboxylic groups, obtained by the alkaline hydrolysis of the ester groups, were studied. Divinylbenzene and N,N′‐methylenebisacrylamide were used as crosslinkers. The starting copolymers and the corresponding ion exchangers were characterized by IR spectroscopy, swelling behavior, and thermogravimetric analysis. The ion‐exchanger properties were correlated with the crosslinker nature and the chemical reactions performed on the AA copolymers. The average molecular weight between two crosslinks, determined from the swelling data in water, was compared with that calculated on the basis of the copolymerization stoichiometry only for the carboxylic cation exchangers. In this way, the preservation of the crosslink density after the hydrolysis was revealed. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 89: 2701–2707, 2003     

Occurrence patterns of alien freshwater turtles in a large urban pond ‘Archipelago’ (Rome,Italy): Suggesting hypotheses on root causes

The patterns of the occurrence and distribution of alien freshwater turtle species in an urban pond archipelago (Rome, Italy) were analysed, with the aim of exploring the role of a set of factors (type of ponds, landscape context, size area, distance from the nearest road) with a generalized linear model approach. A total of 311 ponds subdivided in three types (fountains, small basins, lakes) embedded in different landscape contexts (public parks, private parks, urban areas) at differing distances from the nearest road were sampled. Six non‐native freshwater turtle species in 31 sites were recorded (9.97%). Lakes exhibited the highest occurrence rates of alien freshwater turtles, compared to small basins and fountains. Freshwater turtle species in urbanized areas were only observed in parks (both public and private). In both the public and private parks, the lakes exhibited the highest percentage of occupied sites, with fountains being the lowest. A direct and significant relationship was observed between pond size and species richness. The distance from the nearest road did not appear to affect species richness. A first interpretation of the data from this study facilitated the postulation of two a posteriori hypotheses that should be tested, as follows: (i) the causal process of turtle release is random, and the rate of extinction (and recapture) is higher in smaller ponds, thus producing the observed pattern; and (ii) the turtle release is not random, and people actively select the ponds they consider more suitable for their pet animals. In this study, it appears the lakes were perceived by those who abandon their pets as the most ecologically suitable habitats among other pond types to accommodate the different species of turtles. Knowledge of people's attitudes in regard to releasing pet animals also might assist managers of public green spaces to develop strategies aimed to preserve local biodiversity, and to educate the public about the conservation issue represented by the alien species.