Modelling CreA protein–DNA recognition determinants. A molecular dynamics study of fully charged CreA–DNA model in water

CreA, the negative regulator mediating carbon catabolism repression in Aspergillus nidulans, is a protein that contains a DNA-binding domain comprising two zinc finger motifs. A 3D model for the CreA–G4 (5′-GCGGGGGCGT-3′) complex is constructed on the basis of the structure of the Zif268–DNA crystal complex [Science 252 (1991) 809] and using similarity analysis and computer assisted modelling techniques. The CreA–G4 model was then subjected to a set of molecular dynamics (MD) studies. Based on our previous nano second long Zif268–DNA MD simulation, a 170 ps long trajectory was deemed sufficient to test possible DNA–protein interactions. A screening of the static model and of the trajectory was performed for protein amino acids, nucleotide bases, phosphates backbone and water molecules mediating protein–DNA contacts. Energy, root mean square deviation (RMSD), principal inertial moment and distances were analysed. For this time span, the stability shown in fluctuation patterns reveals the presence of a complex behaving in a manner similar to Zif268–DNA.

An unambiguous characterisation of the amino acids involved in DNA-binding was obtained. These results could contribute towards the establishment of a code of protein–DNA recognition for this class of DNA-binding motifs.     

Electrochemical Oxidation of Guanosine and Xanthosine at Physiological pH: Further Evidences of a Convergent Mechanism for the Oxidation of Purine Nucleosides

The electrochemical oxidation of guanosine and xanthosine, which only differ in the presence of an oxygen atom at C2 position instead of an amine group, is studied on pyrolytic graphite electrodes at different electrolysis time scales in solutions of physiological pH. The oxidation products adsorbed on the electrode surface were electrochemical characterized in terms of variation of the formal potential with pH and catalytic activity towards the oxidation of NADH. The results were compared with those previously described for the oxidation of guanosine and adenosine in alkaline solutions. A common oxidation product is described, the oxidized form of 9‐β‐D ‐ribofuranosyluric acid, which is proposed as the point of convergence in the oxidation routes of all three purine nucleosides.     

Comparative Study of HRP,a Peroxidase‐Mimicking DNAzyme,and ALP as Enzyme Labels in Developing Electrochemical Genosensors for Pathogenic Bacteria

A comparative evaluation of an electrochemical sandwich genoassay for pathogenic bacteria based on immobilized hairpin DNA probes and three different enzyme labels (horseradish peroxidase, alkaline phosphatase and a biomimetic peroxidase‐like DNAzyme) is reported. The natural enzymes were used as streptavidin conjugates, coupled to the surface duplex by using a biotin‐labeled signaling probe, whereas the DNAzyme was directly incorporated to the sequence of the signaling probe. HRP provides enhanced sensitivity although the choice of a catalytic reporter DNA sequence could simplify the assay.     

Apoptosis process in mouse Leydig cells during postnatal development.

The development of Leydig cells in mammals has been widely described as a biphasic pattern with two temporally mature Leydig cell populations, fetal stage followed by the adult generation beginning at puberty. In the present study, mouse Leydig cells were examined for apoptosis during postnatal testis development using electron microscopy and in situ DNA fragmentation by terminal deoxynucleotidyl transferase staining (TdT). Both the morphological study and the DNA fragmentation analysis showed that cellular death by apoptosis did not occur in Leydig cells during the neonatal, prepubertal, puberty, and adult periods. From these results, we suggest that the remaining fetal Leydig cells in the neonatal testis are associated with the involution or degeneration processes. In contrast, in the prepubertal and puberty stages, fragmentation of apoptotic DNA was detected in germ cells present in some seminiferous tubules.     

Keeping an eye on myocilin: a complex molecule associated with primary open-angle glaucoma susceptibility

MYOC encodes a secretary glycoprotein of 504 amino acids named myocilin. MYOC is the first gene to be linked to juvenile open-angle glaucoma (JOAG) and some forms of adult-onset primary open-angle glaucoma (POAG). The gene was identified as an up-regulated molecule in cultured trabecular meshwork (TM) cells after treatment with dexamethasone and was originally referred to as trabecular meshwork-inducible glucocorticoid response (TIGR). Elevated intraocular pressure (IOP), due to decreased aqueous outflow, is the strongest known risk factor for POAG. Increasing evidence showed that the modulation of the wild-type (wt) myocilin protein expression is not causative of glaucoma while some misfolded and self-assembly aggregates of mutated myocilin may be associated with POAG in related or unrelated populations. The etiology of the disease remains unclear. Consequently, a better understanding of the molecular mechanisms underlying POAG is required to obtain early diagnosis, avoid potential disease progression, and develop new therapeutic strategies. In the present study, we review and discuss the most relevant studies regarding structural characterizations, expressions, molecular interactions, putative functions of MYOC gene and/or its corresponding protein in POAG etiology.     

Analysis and thermal optimization of an ecological ventilated self-weighted wood panel for roofs by FVM

This work is to study the performance of an ecological ventilated self-weighted wood panel used on roofs in order to get a high energy savings. With this aim, we have carried out a convective heat transfer analysis of the panel by the finite volume method (FVM). Pure conduction is found in the wood panel through their thermal properties. Heat transfer by convection is always accompanied by conduction, that is to say, among the external air and the upper internal surface of the panel, and the internal air and the inner lower surface of the panel taking into account the heat conduction of the internal ribs. The finite volume method (FVM) is a method for representing and evaluating partial differential equations as algebraic equations. Similar to the finite difference method, values are calculated at discrete places on a meshed geometry. ‘Finite volume’ refers to the small volume surrounding each node point on a mesh. In the finite volume method, volume integrals in a partial differential equation that contain a divergence term are converted to surface integrals, using the divergence theorem. These terms are then evaluated as fluxes at the surfaces of each finite volume. Because the flux entering a given volume is identical to that leaving the adjacent volume, these methods are conservative. One advantage of the finite volume method over the finite difference method is that it does not require a structured mesh, although a structured mesh can be used. The FVM can solve problems on irregular geometries. Furthermore, one advantage of the finite volume method over the finite element method is that it can conserve the variables on a coarse mesh easily. This is an important characteristic for fluid problems just as in this case. Finally, conclusions of this study are exposed.     

One-pot synthesis of a chitosan-based hydrogel as a potential device for magnetic biomaterial

This describes the cross-linking/co-polymerization reaction of chitosan (CS), acrylic acid (AAc), and N, N′-methylenebisacrylamide (MBA) in the presence of citrate-covered-γ-Fe₂O₃ nanoparticules. A gelling process was verified by means of spectroscopic methods; Fourier transform infrared (FT-IR) and solid-state ¹³C-CP/MAS nuclear magnetic resonance (NMR). The corresponding signals of the gelling process, in the ¹³C NMR spectra, for the magnetic hydrogel were shifted to lower values due to embedding of the citrate-covered-γ-Fe₂O₃ nanoparticules. The X-ray diffraction (XRD) confirmed that the crystallinity of the magnetic hydrogel exhibited a different crystalline structure to that without magnetic properties. The Mössbauer and magnetization analysis revealed that the magnetic hydrogel displays a high lattice strain, due to bonded iron atom covalence and superparamagnetism. From scanning electronic microscope (SEM) micrographs, no separation phase coexists between the magnetic nanoparticules and cross-linked hydrogel, indicating an excellent dispersion throughout the hydrogel. The swelling rate was dependent on the cross-linking degree of the hydrogel and ionic strength of the aqueous solution.     

Organization and quantification of the elements in the intertubular space in the adult jaguar testis (Panthera onca, LINNAEUS, 1758)

The endocrine portion of mammal testicle is represented by Leydig cells which, together with connective cells, leukocytes, blood and lymphatic vessels, form the intertubular space. The arrangement and proportion of these components vary in the different species of mammals and form mechanisms that keep the testosterone level – the main product of the Leydig cell – two to three times higher in the interstitial fluid than in the testicular blood vessels and 40–250 times higher in these than in the peripheral blood. Marked differences are observed among animal species regarding the abundance of Leydig cells, loose connective tissue, development degree and location of the lymphatic vessels and their topographical relationship with seminiferous tubules. In the jaguar about 13% of the testicular parenchyma is occupied by Leydig cells, 8.3% by connective tissue and 0.3% by lymphatic vessels. Although included in standard II, as described in the literature, concerning the arrangement of the intertubular space, the jaguar has grouped lymphatic vessels in the intertubular space instead of isolated ones. In the jaguar the average volume of the Leydig cell was 2386 μm3 and its average nuclear diameter was 7.7 μm. A great quantity of 2.3 μm diameter lipidic drops was observed in the Leydig cell cytoplasm of the jaguar. The Leydig cells in the jaguar occupy an average 0.0036% of the body weight and the average number per gram of testicle was within the range for most mammals: between 20 and 40 million.     

Effect of Edible Onion (Allium cepa L.) Film on Quality,Sensory Properties and Shelf Life of Beef Burger Patties

The production of edible film from onion (Allium cepa L.) to be applied as packaging is attractive, due to its chemical properties and biodegradable characteristics. Thus, we tested the hypothesis that edible onion film can positively influence the sensory properties, quality and increasing shelf life of beef burgers patties. The experiment was designed in a 4 × 2 factorial scheme, with two treatments (beef burgers patties with or without edible onion film) at an interval of four storage times (0, 3, 6 and 9 days) at 4 °C. The uncoated burger patties (control) suffered the most intense color modifications during the storage (p < 0.05). The luminosity index was higher (p < 0.05) in the control at all storage times, except at day 6, and redness, yellowness and chrome were higher (p < 0.05) in the edible onion film patties at all storage times. The pH of the beef burger patties was lower (p < 0.05) at all storage times when the edible onion film was applied. For the texture profile, only the chewiness was affected, as the inclusion of the edible onion film improved the chewing of the beef burgers patties over the storage time (p < 0.05). Additionally, there was an inhibition of the microbial growth of mesophiles and psychrophiles with the application of the edible onion film in beef burgers patties. The use of edible onion film improved the perception of panelists for the variables texture, color, flavor, odor and overall appearance, and increased the preference of panelists. The edible onion film is recommended for preserving beef burgers patties, as it delays the proliferation of unwanted microorganisms, stabilizes and improves the color parameters and sensory attributes, and increases the overall acceptance of the consumer.     

Identification of Coumarins and Antimicrobial Potential of Ethanolic Extracts of Dipteryx odorata and Dipteryx punctata

Dipteryx odorata and Dipteryx punctata are species native to the Amazonian, traded by extractivists to obtain coumarin. We aimed to analyze the presence of coumarin in the ethanolic extracts of leaves, branches and fruits of D. odorata and D. punctata and to evaluate the antimicrobial activity of these extracts against phytopathogenic fungi and bacteria of clinical interest. Chemical analyses were performed by thin layer chromatography (TLC) and by gas chromatography coupled to mass spectrometry (GC-MS). For the antifungal assays, the fungi used were Cercospora longissima, Colletotrichum gloeosporioides, two isolates of Fusarium spp. and Sclerotium rolfsii, and the antibacterial assay was performed using the minimum inhibitory concentration (MIC) test with Burkholderia cepacia, Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus bacteria. In D. odorata seed extracts and in D. punctata husks, endocarps, and seeds, we identified 1,2-benzopyrone. D. odorata endocarp extracts and D. punctata seeds provided the greatest decrease in mycelial growth of the evaluated phytopathogens, showing promise as an alternative control. The husk and endocarp extracts of both species had a weak effect on E. coli. This research is the first to compare the different parts of species of the genus Dipteryx and to evaluate the use of husks and endocarps of D. punctata fruits to obtain coumarin. Chemical analyses used to quantify the compounds existing in the extracts, and tests with phytopathogens in vitro and in vivo are currently being carried out.