Coarse-Grained and Atomistic MD Simulations of RNA and DNA Folding

Although the main features of the protein folding problem are coming into clearer focus, the microscopic viewpoint of nucleic acid folding mechanisms is only just beginning to be addressed. Experiments, theory, and simulations are pointing to complex thermodynamic and kinetic mechanisms. As is the case for proteins, molecular dynamics (MD) simulations continue to be indispensable tools for providing a molecular basis for nucleic acid folding mechanisms. In this review, we provide an overview of biomolecular folding mechanisms focusing on nucleic acids. We outline the important interactions that are likely to be the main determinants of nucleic acid folding energy landscapes. We discuss recent MD simulation studies of empirical force field and Go-type MD simulations of RNA and DNA folding mechanisms to outline recent successes and the theoretical and computational challenges that lie ahead.     

Aquaporins Are One of the Critical Factors in the Disruption of the Skin Barrier in Inflammatory Skin Diseases

The skin is the largest organ of the human body, serving as an effective mechanical barrier between the internal milieu and the external environment. The skin is widely considered the first-line defence of the body, with an essential function in rejecting pathogens and preventing mechanical, chemical, and physical damages. Keratinocytes are the predominant cells of the outer skin layer, the epidermis, which acts as a mechanical and water-permeability barrier. The epidermis is a permanently renewed tissue where undifferentiated keratinocytes located at the basal layer proliferate and migrate to the overlying layers. During this migration process, keratinocytes undertake a differentiation program known as keratinization process. Dysregulation of this differentiation process can result in a series of skin disorders. In this context, aquaporins (AQPs), a family of membrane channel proteins allowing the movement of water and small neutral solutes, are emerging as important players in skin physiology and skin diseases. Here, we review the role of AQPs in skin keratinization, hydration, keratinocytes proliferation, water retention, barrier repair, wound healing, and immune response activation. We also discuss the dysregulated involvement of AQPs in some common inflammatory dermatological diseases characterised by skin barrier disruption.     

Monitoring the bacterial population dynamics during fermentation of artisanal Argentinean sausages

The dynamics of the microbial community responsible for the artisanal fermentation of dry sausage produced in Argentina was investigated by using classical and molecular approaches. The combined use of RAPD analysis with primers M13, XD9, RAPD1 and RAPD2 and 16S rDNA sequencing were applied to the identification and intraspecific differentiation of 100 strains of lactobacilli and Micrococcaceae. DGGE analysis was used to monitor the dynamic changes in population after total microbial DNA was directly extracted from sausages and subjected to PCR using V3f (GC), Bact-0124f-GC and Univ-0515r primers. The sequence analysis of 16S rDNA of the dominant species was also carried out. Lactobacillus sakei and Lactobacillus plantarum were the dominant lactic acid organisms during the fermentation while Staphylococcus saprophyticus represented the dominant species of Micrococcaceae. It was demonstrated that the ripening process of Argentinean artisanal fermented sausage is driven by a limited number of Lactobacillus and Staphylococcus strains selected from environmental microbiota by the ability to best compete under the prevailing conditions of the ecological niche. The identification of dominant communities present in this artisanal fermented sausage can help in the selection of starter cultures consisting in well adapted strains to the particular production technology.     

Processing of tomato: impact on in vitro bioaccessibility of lycopene and textural properties

BACKGROUND: Human studies have demonstrated that processing of tomato can greatly increase lycopene bioavailability. However, the difference between processing methods is not widely investigated. In the current study different thermal treatments of tomato were evaluated with regard to their impact on in vitro bioaccessibility and retention of lycopene and β‐carotene as well as textural properties. Thermal treatments used were low (60 °C) and high (90 °C) temperature blanching followed by boiling. RESULTS: Lycopene was relatively stable during thermal treatment, whereas β‐carotene was significantly (P < 0.05) reduced by all heat treatments except for low temperature blanching. In vitro bioaccessibility of lycopene was significantly increased from 5.1 ± 0.2 to 9.2 ± 1.8 and 9.7 ± 0.6 mg kg^?1 for low and high temperature blanching, respectively. An additional boiling step after blanching did not further improve lycopene bioaccessibility for any treatment, but significantly reduced the consistency of low temperature treated samples. CONCLUSION: Choice and order of processing treatments can have a large impact on both lycopene bioavailability and texture of tomato products. Further investigations are needed, but this study provides one of the first steps towards tomato products tailored to optimise nutritional benefits. Copyright © 2010 Society of Chemical Industry     

Phage types, virulence genes and PFGE profiles of Shiga toxin-producing Escherichia coli O157:H7 isolated from raw beef, soft cheese and vegetables in Lima (Peru)

The present study was conducted in Lima Metropolitana to evaluate the prevalence of Shiga toxin-producing Escherichia coli (STEC) O157:H7 in raw beef, raw ground beef, soft cheese and fresh vegetables, sampled at different markets in the city. Between October 2000 and February 2001, 407 food samples were collected from different markets in the 42 districts of Lima Metropolitana. Samples were assayed for E. coli O157 by selective enrichment in modified Tryptic Soy Broth containing novobiocin, followed by immunomagnetic separation (IMS) and plating onto sorbitol MacConkey agar supplemented with cefixime and potassium tellurite. Fifty (12.3%) of 407 food samples resulted positive for E. coli O157 isolation (23 of 102 ground beef; 15 of 102 beef meat; eight of 102 soft cheese and four of 101 fresh vegetables). Thirty-five E. coli O157 isolates were further analysed for the presence of virulence genes. All 35 were positive by PCR for O157 rfbE, fliCh7, eae-gamma1 and ehxA genes. In addition, genes encoding Shiga toxins were detected in 33 of 35 isolates, five isolates (14%) encoded stx(1), stx(2), and 28 (80%) stx2 only. The isolates were of seven different phage types (PT4, PT8, PT14, PT21, PT34, PT54, and PT87) with three phage types accounting for 80% of isolates: PT4 (15 isolates), PT14 (8 isolates), and PT21 (5 isolates). Interestingly, the majority (31 of 35; 89%) of E. coli O157:H7 isolates characterized in this study belonged mainly to the phage types previously found in STEC O157:H7 strains associated with severe human disease in Europe and Canada. Pulsed-field gel electrophoresis (PFGE) of 32 isolates revealed 14 XbaI-PFGE groups (I to XIV) of similarity >85%, with 23 (72%) isolates grouped in five clusters. Some isolates from different districts presented a high clonal relatedness. Thus, PFGE group VIII clustered eleven strains from nine different districts. The broad range of PFGE subtypes found in this study demonstrates the natural occurrence of many genetic variants among STEC O157:H7 spread in Lima.     

Evaluation of in vitro antioxidant properties of some traditional Sardinian medicinal plants: Investigation of the high antioxidant capacity of Rubus ulmifolius

The antioxidant capacities of 11 botanical species used in the tradition of Sardinia as teas beverages or as decoction for medicinal purposes were evaluated using different in vitro methods (BR, TEAC, DPPH and FC). Among the various species, Rubus ulmifolius, resulted the more active with all the used methods. Phytochemical investigation on the extract yields in the isolation of several phenolic compounds namely caffeic acid, ferulic acid, quercetin-3-O-glucuronide, kaempferol-3-O-glucuronide, kaempferol-3-O-(6″-p-coumaroyl)-β-d-glucopyranoside, kaempferol-3-O-(6″-caffeoyl)-β-d-glucopyranoside, chlorogenic acid, 4-caffeoylquinic acid and 5-caffeoylquinic acid. The antioxidant activity of isolated compounds was also evaluated.     

Optimization and Validation of a UV–HPLC Method for Vitamin C Determination in Strawberries (<Emphasis Type="Italic">Fragaria ananassa</Emphasis> Duch.), Using Experimental Designs

Vitamin C or total ascorbic acid (TAA) in fruits can be assumed as ascorbic acid (AA) plus dehydroascorbic acid (DHA) content. The aim of this work was to optimize and validate, using experimental designs, a new high-performance liquid chromatographic method for vitamin C determination in strawberries. The mobile phase (MP) consisted of a 0.03 M sodium acetate/acetic acid buffer, 5% methanol. For optimization, a Box–Behnken design was used (three factors at three levels: (a) pH of MP, 3.8–5.8; (b) wavelength, 240–270 nm; and (c) flow rate, 0.5–1.2 ml min⁻¹). Responses were: AA and TAA areas, peak widths, and retention times. A global optimization was performed using the Derringer desirability function, and a value of 0.84 was reached for the combination of design factors: A = 5.8, B = 251 nm, and C = 1.15 ml min⁻¹. Method validation, using AA standard solutions, included: linearity study, limits of detection and quantification, and calibration and analytical sensitivity quantifications. Precision and accuracy were studied in strawberry extracts. The coefficients of variation (percent) were: AA, 1.5%; TAA, 1.8%, and DHA, 4.9%. Accuracy was evaluated with AA standard spiked in 30–150% range of the expected amount of analyte in real samples. The joint confidence elliptical region test and t test were employed for the study of the difference between recoveries (percent) and the ideal 100%. The robustness was analyzed using a fractional factorial design (3⁴⁻²), and an AA recovery study after slight changes in operative variables was performed. The results indicate that the optimized method was linear, sensible, precise, accurate, and robust.     

Densification and Thermal Conductivity of AIN Doped with Y2O3, CaO, and Li2O

Small amounts of Li₂O result in sintering in the AIN-Y₂O₃-CaO and AIN-CaO systems at firing temperatures <1600°C. The effect is ascribed to reduction of the liquidus temperature. Furthermore, Li₂O is removed by volatization at temperatures from 1300° to 1600°C, and its content decreases several ppm from the initial 0.3 wt%. Li₂O-doped AIN specimens containing Y₂O₃ and CaO additives are well densified by firing at 1600°C for 6 h, and their thermal conductivity is 135 W^.m^−1.K⁻¹.The effect of Li₂O addition on sintering and thermal conductivity also is discussed through thermo-dynamic considerations.     

Achieving the Sustainable Development Goals: improving water services in cities affected by extreme weather events

Abstract

This article discusses how key risks from extreme weather events might affect progress towards meeting Sustainable Development Goals 6 and 11 in cities in developing countries. It outlines the magnitude of the existing shortfall in safe water and sanitation services, and how climate change will exacerbate existing problems. It argues that the performance of many governments thus far has lacked urgency and purpose. Unless governments in particular become more committed, with redoubled effort, the goals are unlikely to be achieved.     

Design and Characterization of Myristoylated and Non-Myristoylated Peptides Effective against Candida spp. Clinical Isolates

The increasing resistance of fungi to antibiotics is a severe challenge in public health, and newly effective drugs are required. Promising potential medications are lipopeptides, linear antimicrobial peptides (AMPs) conjugated to a lipid tail, usually at the N-terminus. In this paper, we investigated the in vitro and in vivo antifungal activity of three short myristoylated and non-myristoylated peptides derived from a mutant of the AMP Chionodracine. We determined their interaction with anionic and zwitterionic membrane-mimicking vesicles and their structure during this interaction. We then investigated their cytotoxic and hemolytic activity against mammalian cells. Lipidated peptides showed a broad spectrum of activity against a relevant panel of pathogen fungi belonging to Candida spp., including the multidrug-resistant C. auris. The antifungal activity was also observed vs. biofilms of C. albicans, C. tropicalis, and C. auris. Finally, a pilot efficacy study was conducted on the in vivo model consisting of Galleria mellonella larvae. Treatment with the most-promising myristoylated peptide was effective in counteracting the infection from C. auris and C. albicans and the death of the larvae. Therefore, this myristoylated peptide is a potential candidate to develop antifungal agents against human fungal pathogens.