Probing the Ion Binding Site in a DNA Holliday Junction Using F?rster Resonance Energy Transfer (FRET)

Holliday Junctions are critical DNA intermediates central to double strand break repair and homologous recombination. The junctions can adopt two general forms: open and stacked-X, which are induced by protein or ion binding. In this work, fluorescence spectroscopy, metal ion luminescence and thermodynamic measurements are used to elucidate the ion binding site and the mechanism of junction conformational change. Förster resonance energy transfer measurements of end-labeled junctions monitored junction conformation and ion binding affinity, and reported higher affinities for multi-valent ions. Thermodynamic measurements provided evidence for two classes of binding sites. The higher affinity ion-binding interaction is an enthalpy driven process with an apparent stoichiometry of 2.1 ± 0.2. As revealed by Eu³⁺ luminescence, this binding class is homogeneous, and results in slight dehydration of the ion with one direct coordination site to the junction. Luminescence resonance energy transfer experiments confirmed the presence of two ions and indicated they are 6–7 Å apart. These findings are in good agreement with previous molecular dynamics simulations, which identified two symmetrical regions of high ion density in the center of stacked junctions. These results support a model in which site-specific binding of two ions in close proximity is required for folding of DNA Holliday junctions into the stacked-X conformation.     

Applicability of the generalized scaling law to a pile-inclined ground system subject to liquefaction-induced lateral spreading

The generalized scaling law is based on the concept of two-stage scaling and allows currently available centrifuge facilities to model a large-scale prototype expanding over the spatial dimension ranging from 30 m or larger subject to earthquake motions. This paper presents the results of investigation on the applicability of the generalized scaling law to the fully nonlinear regime of soil-structure system with the induced strain level of 10% in the order of magnitude. The centrifuge model tests performed in this study under the modeling of models scheme consist of a pile model embedded in a inclined ground subject to liquefaction-induced lateral spreading. Four different centrifugal accelerations ranging from 13g to 50g are used whereas the actual size of the physical model is kept constant with an overall scaling factor of 1/100. The models are exposed to tapered sinusoidal input accelerations of frequency 0.59 Hz and amplitude 3.0 m/s² in prototype scale, and the results are compared in terms of prototype by applying the generalized scaling law. As for the response of the ground during shaking, essentially identical accelerations and excess pore water pressures are recorded for all cases, while the lateral displacement shows a variation ranging from 5% to 9% in terms of shear strain due to a slight variation in experimental conditions (e.g., input peak acceleration, achieved density distribution). Practically the same responses are measured among the cases in the dissipation phase of excess pore water pressure. With regard to pile behavior, nearly identical responses for the lateral displacements and bending moments are obtained for all cases both during and after shaking. These results demonstrated that the generalized scaling law is applicable to the fully nonlinear regime of soil-structure system subject to the cumulative shear strain in the order of 10% due to cyclic mobility of sands during earthquakes.     

Effect of Tempering on the Oxidation Behaviour of a Roll-Grade High-Speed Steel During Thermal Cycling

Oxidation of Metals - The oxidation characteristics of a roll-grade high-speed steel with different tempering heat treatments were studied under thermal cycling conditions at 650 °C...     

Simultaneous oxidation of aromatic compounds using Sr-doped lanthanum manganites as catalysts

Strontium-doped lanthanum manganites, La_1-xSr_xMnO₃ (LSMO), are promising and affordable catalysts for oxidative degradation of volatile organic compounds. LSMO catalysts (x = 0, .1, .2, and .3) were prepared by the citrate-nitrate autocombustion (CNA) and coprecipitation synthesis. The phase composition was confirmed by X-ray diffraction and Rietveld refinement analysis, while the oxygen content was determined by Mohr's salt permanganate titration. Morphology and porosity of prepared catalysts was correlated to catalytic oxidation of benzene, toluene, ethylbenzene and o-xylene. It was observed that both synthesis methods yielded catalysts of similar average pore size diameter and specific surface area, but the pore size distribution differed: CNA-prepared catalysts had a multimodal pore size distribution, while the coprecipitated ones had a single maximum at 4 nm. Catalysts prepared by the CNA method have shown a higher catalytic activity in the temperature range 373–723 K, as the presence of Mn³⁺/Mn⁴⁺ mixed valences increased their reducibility.     

Synthetic Activity of Recombinant Whole Cell Biocatalysts Containing 2-Deoxy-D-ribose-5-phosphate Aldolase from Pectobacterium atrosepticum

In nature 2-deoxy-D-ribose-5-phosphate aldolase (DERA) catalyses the reversible formation of 2-deoxyribose 5-phosphate from D-glyceraldehyde 3-phosphate and acetaldehyde. In addition, this enzyme can use acetaldehyde as the sole substrate, resulting in a tandem aldol reaction, yielding 2,4,6-trideoxy-D-erythro-hexapyranose, which spontaneously cyclizes. This reaction is very useful for the synthesis of the side chain of statin-type drugs used to decrease cholesterol levels in blood. One of the main challenges in the use of DERA in industrial processes, where high substrate loads are needed to achieve the desired productivity, is its inactivation by high acetaldehyde concentration. In this work, the utility of different variants of Pectobacterium atrosepticum DERA (PaDERA) as whole cell biocatalysts to synthesize 2-deoxyribose 5-phosphate and 2,4,6-trideoxy-D-erythro-hexapyranose was analysed. Under optimized conditions, E. coli BL21 (PaDERA C-His AA C49M) whole cells yields 99 % of both products. Furthermore, this enzyme is able to tolerate 500 mM acetaldehyde in a whole-cell experiment which makes it suitable for industrial applications.     

Isothermal and non‐isothermal crystallization of poly(L‐lactic acid)/poly(butylene terephthalate) blends

Isothermal and non‐isothermal crystallization kinetics of poly(l ‐lactic acid)/poly(butylene terephthalate) (PLLA/PBT) blends containing PLLA as major component is detailed in this contribution. PLLA and PBT are not miscible, but compatibility of the polymer pair is ensured by interactions between the functional groups of the two polyesters, established upon melt mixing. Crystal polymorphism of the two polyesters is not influenced by blending, as probed by wide‐angle X‐ray analysis. The addition of PLLA does not affect the temperature range of crystallization kinetics of PBT, nor the crystallinity level attained when the blends are cooled from the melt at constant rate. Conversely, PBT favors crystallization of the biodegradable polyester. The addition of PBT results in an anticipated onset of crystallization of PLLA during cooling at a fixed rate, with a sizeable enhancement of the crystal fraction. Isothermal crystallization analysis confirmed the faster crystallization rate of PLLA in the presence of PBT. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014 , 131, 40372.     

Pullulan‐based films and coatings for food packaging: Present applications,emerging opportunities,and future challenges

Societal and industrial demands for lower environmental impact, cost effectiveness, and high‐performance goods and services are increasingly impacting the choice of technologies which are developed and deployed in consumer products. Like many other sectors, food packaging is moving to new technologies; the use of biopolymers is one of the most promising strategies toward an optimized use of traditional packaging materials (e.g., oil‐based plastics) without impairing the goal of extending shelf life. Among other food packaging materials, pullulan is attracting much attention due to its unique features. The goal of this review is to provide an overview of current and emerging applications of pullulan within the food packaging sector. In particular, the functional properties of interest for the food packaging industry will be discussed in light of the physicochemical attributes of this exopolysaccharide. Future challenges that may dictate the successful penetration of pullulan in the food packaging market are also outlined. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014 , 131, 40539.     

A Modular Composite Device of Poly(Ethylene Oxide)/Poly(Butylene Terephthalate) (PEOT/PBT) Nanofibers and Gelatin as a Dual Drug Delivery System for Local Therapy of Soft Tissue Tumors

In the clinical management of solid tumors, the possibility to successfully couple the regeneration of injured tissues with the elimination of residual tumor cells left after surgery could open doors to new therapeutic strategies. In this work, we present a composite hydrogel–electrospun nanofiber scaffold, showing a modular architecture for the delivery of two pharmaceutics with distinct release profiles, that is potentially suitable for local therapy and post-surgical treatment of solid soft tumors. The composite was obtained by coupling gelatin hydrogels to poly(ethylene oxide)/poly(butylene terephthalate) block copolymer nanofibers. Results of the scaffolds’ characterization, together with the analysis of gelatin and drug release kinetics, displayed the possibility to modulate the device architecture to control the release kinetics of the drugs, also providing evidence of their activity. In vitro analyses were also performed using a human epithelioid sarcoma cell line. Furthermore, publicly available expression datasets were interrogated. Confocal imaging showcased the nontoxicity of these devices in vitro. ELISA assays confirmed a modulation of IL-10 inflammation-related cytokine supporting the role of this device in tissue repair. In silico analysis confirmed the role of IL-10 in solid tumors including 262 patients affected by sarcoma as a negative prognostic marker for overall survival. In conclusion, the developed modular composite device may provide a key-enabling technology for the treatment of soft tissue sarcoma.     

ICA1L Is Associated with Small Vessel Disease: A Proteome-Wide Association Study in Small Vessel Stroke and Intracerebral Haemorrhage

Small vessel strokes (SVS) and intracerebral haemorrhages (ICH) are acute outcomes of cerebral small vessel disease (SVD). Genetic studies combining both phenotypes have identified three loci associated with both traits. However, the genetic cis-regulation at the protein level associated with SVD has not been studied before. We performed a proteome-wide association study (PWAS) using FUSION to integrate a genome-wide association study (GWAS) and brain proteomic data to discover the common mechanisms regulating both SVS and ICH. Dorsolateral prefrontal cortex (dPFC) brain proteomes from the ROS/MAP study (N = 376 subjects and 1443 proteins) and the summary statistics for the SVS GWAS from the MEGASTROKE study (N = 237,511) and multi-trait analysis of GWAS (MTAG)-ICH–SVS from Chung et al. (N = 240,269) were selected. We performed PWAS and then a co-localization analysis with COLOC. The significant and nominal results were validated using a replication dPFC proteome (N = 152). The replicated results (q-value < 0.05) were further investigated for the causality relationship using summary data-based Mendelian randomization (SMR). One protein (ICA1L) was significantly associated with SVS (z-score = −4.42 and p-value = 9.6 × 10⁻⁶) and non-lobar ICH (z-score = −4.8 and p-value = 1.58 × 10⁻⁶) in the discovery PWAS, with a high co-localization posterior probability of 4. In the validation PWAS, ICA1L remained significantly associated with both traits. The SMR results for ICA1L indicated a causal association of protein expression levels in the brain with SVS (p-value = 3.66 × 10⁻⁵) and non-lobar ICH (p-value = 1.81 × 10⁻⁵). Our results show that the association of ICA1L with SVS and non-lobar ICH is conditioned by the cis-regulation of its protein levels in the brain.     

An Experimental Model of Neuro–Immune Interactions in the Eye: Corneal Sensory Nerves and Resident Dendritic Cells

The cornea is an avascular connective tissue that is crucial, not only as the primary barrier of the eye but also as a proper transparent refractive structure. Corneal transparency is necessary for vision and is the result of several factors, including its highly organized structure, the physiology of its few cellular components, the lack of myelinated nerves (although it is extremely innervated), the tightly controlled hydration state, and the absence of blood and lymphatic vessels in healthy conditions, among others. The avascular, immune-privileged tissue of the cornea is an ideal model to study the interactions between its well-characterized and dense sensory nerves (easily accessible for both focal electrophysiological recording and morphological studies) and the low number of resident immune cell types, distinguished from those cells migrating from blood vessels. This paper presents an overview of the corneal structure and innervation, the resident dendritic cell (DC) subpopulations present in the cornea, their distribution in relation to corneal nerves, and their role in ocular inflammatory diseases. A mouse model in which sensory axons are constitutively labeled with tdTomato and DCs with green fluorescent protein (GFP) allows further analysis of the neuro-immune crosstalk under inflammatory and steady-state conditions of the eye.