Bioinformatic Tools for the Analysis and Prediction of ncRNA Interactions

Noncoding RNAs (ncRNAs) play prominent roles in the regulation of gene expression via their interactions with other biological molecules such as proteins and nucleic acids. Although much of our knowledge about how these ncRNAs operate in different biological processes has been obtained from experimental findings, computational biology can also clearly substantially boost this knowledge by suggesting possible novel interactions of these ncRNAs with other molecules. Computational predictions are thus used as an alternative source of new insights through a process of mutual enrichment because the information obtained through experiments continuously feeds through into computational methods. The results of these predictions in turn shed light on possible interactions that are subsequently validated experimentally. This review describes the latest advances in databases, bioinformatic tools, and new in silico strategies that allow the establishment or prediction of biological interactions of ncRNAs, particularly miRNAs and lncRNAs. The ncRNA species described in this work have a special emphasis on those found in humans, but information on ncRNA of other species is also included.     

Development and characterisation of microporous biomimetic scaffolds loaded with magnetic nanoparticles as bone repairing material

Fine-tuning of the scaffolds structural features for bone tissue engineering can be an efficient approach to regulate the specific response of the osteoblasts. Here, we loaded magnetic nanoparticles aka superparamagnetic iron oxide nanoparticles (SPIONs) into 3D composite scaffolds based on biological macromolecules (chitosan, collagen, hyaluronic acid) and calcium phosphates for potential applications in bone regeneration, using a biomimetic approach. We assessed the effects of organic (chitosan/collagen/hyaluronic acid) and inorganic (calcium phosphates, SPIONs) phase over the final features of the magnetic scaffolds (MS). Mechanical properties, magnetic susceptibility and biological fluids retention are strongly dependent on the final composition of MS and within the recommended range for application in bone regeneration. The MS architecture/pore size can be made bespoken through changes of the final organic/inorganic ratio. The scaffolds undertake mild degradation as the presence of inorganic components hinders the enzyme catalytic activity. In vitro studies indicated that osteoblasts (SaOS-2) on MS9 had similar cell behaviour activity in comparison with the TCP control. In vivo data showed an evident development of integration and resorption of the MS composites with low inflammation activity. Current findings suggest that the combination of SPIONs into 3D composite scaffolds can be a promising toolkit for bone regeneration.     

Characterization of homofermentative lactobacilli isolated from kefir grains: potential use as probiotic

Considering that several health promoting properties are associated with kefir consumption and a reliable probiotic product requires a complete identification of the bacterial species, the present work evaluates several proved markers of probiotic potential of eleven isolates of homofermentative lactobacilli isolated from kefir grains and molecular identification and genotypic diversity. Using restriction analysis of amplified ribosomal DNA (ARDRA) and analysis of the 16S-23S rRNA internal spacer region we confirmed that all homofermentative lactobacilli belong to the species Lactobacillus plantarum. RAPD-PCR analysis allowed the discrimination of lactobacilli in five clusters. All isolates exhibited high resistance to bile salt. High survival after one hour of exposure to pH 2.5 was observed in Lb. plantarum CIDCA 8313, 83210, 8327 and 8338. All isolates were hydrophilic and non autoaggregative. Isolate CIDCA 8337 showed the highest percentage of adhesion among strains. All tested lactobacilli had strong inhibitory power against Salmonella typhimurium and Escherichia coli. Seven out of eleven isolates showed inhibition against Sal. enterica and five isolates were effective against Sal. gallinarum. Only CIDCA 8323 and CIDCA 8327 were able to inhibit Sal. sonnei. We did not find any correlation between the five clusters based on RAPD-PCR and the probiotic properties, suggesting that these isolates have unique characteristics.     

Oil recovery and lecithin production using water degumming sludge of crude soybean oils

BACKGROUND: Wet gums produced during aqueous degumming of crude soybean oils are currently processed to produce lecithin or added to meals to increase their nutritive value for animal feed. Oils occluded in these gums are generally not recovered or processed. In this work, three methods to recover occluded oil and obtain lecithin from wet gums were assayed: direct extraction of oil with cold acetone (Method I), extraction after water elimination under vacuum (Method II) and by solvent partition with hexane/ethanol (Method III). RESULTS: Higher oil yields (up to 588 g kg^?1 of occluded oil) were obtained when water was eliminated before extraction (Methods II and III). No significant differences were observed in lecithin yields between three methods (720–807 g kg^?1 of dried gums). Recovered oils had acidity = 16.7–21.7 g kg^?1 as oleic acid, TOTOX (total oxidation) values ≤ 8.82, unsaponifiable matter = 9.0–12.1 g kg^?1, and Phosphorus = 87–330 mg kg^?1. Lecithins obtained by Methods I, II and III hexane phase had the same purity level (610–691 g of total measured phospholipids kg^?1). CONCLUSIONS: The occluded oil in soybean wet gums can be recovered, with quality and stability indexes compatible with their reinsertion in the productive process, by water elimination and extraction with acetone. Lecithins can be obtained with different phospholipid composition and diverse application fields. Copyright © 2008 Society of Chemical Industry     

Effect of γ-radiation on green onion DNA integrity: Role of ascorbic acid and polyphenols against nucleic acid damage

The effect of γ-radiation on green onion DNA integrity, phenol content, oxygen radical absorbance capacity, employing pyrogallol red and fluorescein as probes, as well as ascorbic acid content has been evaluated. Measurements using thiazole orange-DNA fluorescence and agarose gel electrophoresis show that γ-radiation does not lead to an apparent DNA change in green onion. However, it was readily cleaved upon irradiation from the previously isolated nucleic acid. Furthermore, green onion exposure to γ-radiation produces slight increases in the polyphenol concentrations (163–188 μM Trolox eq.) and a decrease in the oxygen radical absorbance using fluorescein (from 245 to 200 Trolox eq.) Interestingly, a high ascorbic acid content (364 μM), which decreases by 40% after γ-ray exposure was measured by using pyrogallol-red-based oxygen radical absorbance capacity induction times from green onion aqueous extracts. Thus, our results suggest that ascorbic acid present in green onion plays a fundamental role in the plant antioxidant response toward γ-radiation exposure, while polyphenols remain largely unchanged, as revealed from oxygen radical absorbance capacity, employing pyrogallol red.     

Shall we dance? How a multicopper oxidase chooses its electron transfer partner

Multicopper oxidases (MCOs) are encoded in the genomes of Eukarya, Bacteria, and Archea. These proteins are unique in that they contain at least four Cu atom prosthetic groups organized into one each of the three spectral classifications of copper sites in biology: type 1 (T1), type 2 (T2), and binuclear type 3 (T3), where the T2 and T3 sites form a trinuclear Cu cluster. With these four redox-active copper sites, the multicopper oxidases catalyze the four-electron (4e(-)) reduction of dioxygen to 2H2O, an activity that they alone share with the terminal heme-containing oxidases. Most MCOs exhibit broad specificity towards organic reductants, while a relatively small number of family members exhibit equally robust activity towards metal ions like Fe(II), Cu(I), and Mn(II) and, thus, are considered metallo-oxidases. This Account analyzes the structure-activity features of multicopper oxidases that determine their relative substrate specificity. Since the substrate oxidation step involves an outer-sphere electron transfer from the reductant to the T1Cu site in the protein, the concepts of Marcus theory are applied to unravel the origin of the substrate specificity of the multicopper ferroxidases.     

Studies on the synthesis of diacetyl over oxidation zeolite catalysts

Diacetyl (2,3-butanedione) synthesis from methyl ethyl ketone over oxidation zeolites using O₂ as oxidant was studied. Various zeolites with Fe, V and Ti as active sites were employed. VS-1, Ti-NCL, Ti-MCM-41 and FeBEA type materials were synthesized and characterized by BET, FTIR, XRD, pyridine adsorption and template desorption. The detailed study of the effect of reaction temperature, the effect of concentration of oxygen and the addition of water was realized. The most active catalyst was zeolites with V as oxidation center.     

Subjective perception of safety in healthy individuals working with 7 T MRI scanners: a retrospective multicenter survey

Objective

To retrospectively assess perception of safety of healthy individuals working with human 7 Tesla (T) magnetic resonance imaging (MRI) scanners.

Materials and methods

A total of 66 healthy individuals with a mean age of 31 ± 7 years participated in this retrospective multicentre survey study. Nonparametric correlation analysis was conducted to evaluate the relation between self-reported perception of safety and prevalence of sensory effects while working with 7 T MRI scanners for an average 47 months.

Results

The results indicated that 98.5 % of the study participants had a neutral or positive feeling about safety aspects at 7 T MRI scanners. 45.5 % reported that they feel very safe and none of the participants stated that they feel moderately or very unsafe while working with 7 T MRI scanners. Perception of safety was not affected by the number of hours per week spent in the vicinity of the 7 T MRI scanner or the duration of experience with 7 T MRI. More than 50 % of individuals experienced vertigo and metallic taste while working with 7 T MRI scanners. However, participants’ perceptions of safety were not affected by the prevalence of MR-related symptoms.

Conclusions

The overall data indicated an average perception of a moderately safe work environment. To our knowledge, this study delineates the first attempt to assess the subjective safety perception among 7 T MRI workers and suggests further investigations are indicated.

     

Synthesis of BaTiO3 by soft chemistry routes

In this paper we report a comparison concerning the properties of BaTiO₃ (BTO) ceramics obtained by two soft chemical routes, modified Pechini method and thermal decomposition of oxalate-based precursor. XRD data show the formation of single phase BaTiO₃ with tetragonal symmetry when the polymeric citrate-based precursor was annealed at 850 °C, 2 h. In the case of oxalate based-precursor, longer thermal treatment is required to obtain BaTiO₃ free of any secondary phases. For BaTiO₃ powders prepared by modified Pechini method, TEM and SEM investigations revealed the obtaining of uniformly sized particles forming spherical agglomerates inside large, non-uniform and partially sintered aggregates. The powders synthesized via oxalate route show particles of various sizes, with the same tendency of spherical agglomerates formation, but unlike the modified Pechini synthesis, more uniform and smaller aggregates with well-defined hexagonal-like shape were noticed. The relative permittivity values of 6,478 and 5,088 at Curie temperatures of 127 and 130 °C and low dielectric losses (tan δ?=?0.012) at room temperature were obtained for ceramic samples synthesized via Pechini method and oxalate route, respectively.