Exploring the mechanisms of graphene oxide behavioral and morphological changes in zebrafish

The presence of natural organic matter such as humic acid (HA) can influence the behavior of graphene oxide (GO) in the aquatic environment. In this study, zebrafish embryos were analyzed after 5 and 7 days of exposure to GO (100 mg L^-1) and HA (20 mg L^-1) alone or together. The results indicated that, regardless of the presence of HA, larvae exposed to GO for 5 days showed an increase in locomotor activity, reduction in the yolk sac size, and total length and inhibition of AChE activity, but there was no difference in enzyme expression. The statistical analysis indicated that the reductions in total larval length, yolk sac size, and AChE activity in larvae exposed to GO persisted in relation to the control group, but there was a recovery of these parameters in groups also exposed to HA. Larvae exposed to GO for 7 days did not show significant differences in locomotor activity, but the RT-PCR gene expression analysis evidenced an increase in the AChE expression. Since the embryos exposed to GO showed a reduction in overall length, they were submitted to confocal microscopy and their muscle tissue configuration investigated. No changes were observed in the muscle tissue. The results indicated that HA is associated with the toxicity risk modulation by GO and that some compensatory homeostasis mechanisms may be involved in the developmental effects observed in zebrafish.

Integrated assessment for establishing an oil environmental vulnerability map: case study for the Santos Basin region, Brazil

The growth of maritime transport and oil exploitation activities may increase the risk of oil spills. Thus, plans and actions to prevent or mitigate impacts are needed to minimize the effects caused by oil. However, tools used worldwide to support contingency plans have not been integrated, thus leading to failure in establishing priority areas. This investigation aimed to develop indices of environmental vulnerability to oil (IEVO), by combining information about environmental sensibility to oil and results of numerical modeling of spilled oil. To achieve that, a case study concerning to oil spills scenarios in a subtropical coastal area was designed, and IEVOs were calculated and presented in maps, in order to make the information about the areas' vulnerability more easily visualized. For summer, the extension of coastline potentially affected by oil was approximately 150 km, and most of the coastline presented medium to high vulnerability. For winter, 230 km coastline would be affected, from which 75% were classified as medium to high vulnerability. Thus, IEVO maps allowed a rapid and clearer interpretation of the vulnerability of the mapped region, facilitating the planning process and the actions in response to an oil spill.

The I-CreI meganuclease and its engineered derivatives: applications from cell modification to gene therapy

Meganucleases (MNs) are highly specific enzymes that can induce homologous recombination in different types of cells, including mammalian cells. Consequently, these enzymes are used as scaffolds for the development of custom gene-targeting tools for gene therapy or cell-line development. Over the past 15 years, the high resolution X-ray structures of several MNs from the LAGLIDADG family have improved our understanding of their protein-DNA interaction and mechanism of DNA cleavage. By developing and utilizing high-throughput screening methods to test a large number of variant-target combinations, we have been able to re-engineer scores of I-CreI derivatives into custom enzymes that target a specific DNA sequence of interest. Such customized MNs, along with wild-type ones, have allowed for exploring a large range of biotechnological applications, including protein-expression cell-line development, genetically modified plants and animals and therapeutic applications such as targeted gene therapy as well as a novel class of antivirals.

Neutralization of the pharmacological effects of bothropstoxin-I from Bothrops jararacussu (jararacuçu) venom by crotoxin antiserum and heparin

Bothropstoxin-I (BthTX-I), the principal myotoxin of Bothrops jararacussu venom, is devoid of phospholipase A(2) (PLA(2)) activity but capable of blocking neuromuscular transmission in mouse nerve-muscle preparations. In this study, the ability of crotoxin antiserum and heparin in preventing the neurotoxic and myotoxic effects of BthTX-I was investigated. Phrenic nerve-diaphragm preparations (PND) stimulated indirectly with supramaximal stimuli (0.2 ms, 0.1 Hz) were incubated with BthTX-I (20 microg/ml) alone or with BthTX-I preincubated with antiserum or heparin for 30 min at 37 degrees C prior to testing. Control preparations were incubated with Tyrode solution, antiserum or heparin alone. BthTX-I (20 microg/ml) produced 50% neuromuscular blockade in the PND preparations in 31+/-4min, with complete blockade occurring in 120 min. The antiserum and heparin significantly prevented the neuromuscular blockade caused by BthTX-I (84 +/- 4% and 100% protection, respectively). Light microscopy examination of the muscles at the end of the 120 min incubation showed that BthTX-I damaged 48 +/- 6% of the fibers. Preincubating the toxin with antivenom significantly reduced the extent of this damage (only 15 +/- 4% of fibers affected, corresponding to 69% protection, P<0.01) whereas heparin offered no protection (34 +/- 7% of fibers affected, not significantly different from that seen with toxin alone). These results show that the antivenom was more effective in neutralizing the myotoxic effects of BthTX-I than was heparin.

Lung tissue mechanics and extracellular matrix remodeling in acute lung injury

This study was undertaken to test whether there is structural remodeling of lung parenchyma that could lead to tissue mechanical changes at an early phase of varying degrees of acute lung injury (ALI). Tissue resistance (R), dynamic elastance (E), and hysteresivity (eta) were analyzed during sinusoidal oscillations of rat lung parenchymal strips 24 h after intraperitoneal injection of saline (C) or paraquat (P [10, 15, 25, and 30 mg/kg]). These strips were also stained in order to quantify the amount of collagen and of three types of elastic fibers (elaunin, oxytalan, and fully developed elastic fibers) in the alveolar septa. E augmented progressively from C to P25, but the data from the P25 and P30 groups were not different (p < 0.0001). R and eta increased from C to P10 and from P15 to P25 (p < 0.001). Collagen fiber content increased exponentially with the severity of the injury. Elaunin and fully developed elastic fibers remained unchanged in the five groups, while oxytalan fibers increased only in the P25 and P30 groups. In conclusion, the pronounced mechanical changes at the tissue level and fibroelastogenesis happened at an early phase of the disease and even in mildly abnormal lung parenchyma.

KEYWORDS

elastance; collagen fibers; elastin; paraquat

Lung tissue mechanics and extracellular matrix composition in a murine model of silicosis

The dynamic mechanical properties of lung tissue and its contents of collagen and elastic fibers were studied in strips prepared from mice instilled intratracheally with saline (C) or silica [15 (S15) and 30 days (S30) after instillation]. Resistance, elastance, and hysteresivity were studied during oscillations at different frequencies on S15 and S30. Elastance increased from C to silica groups but was similar between S15 and S30. Resistance was augmented from C to S15 and S30 and was greater in S30 than in S15 at higher frequencies. Hysteresivity was higher in S30 than in C and S15. Silica groups presented a greater amount of collagen than did C. Elastic fiber content increased progressively along time. This increment was related to the higher amount of oxytalan fibers at 15 and 30 days, whereas elaunin and fully developed elastic fibers were augmented only at 30 days. Silicosis led not only to pulmonary fibrosis but also to fibroelastosis, thus assigning a major role to the elastic system in the silicotic lung.

Crystal structure of the thermostable archaeal intron-encoded endonuclease I-DmoI

I-DmoI is a 22 kDa endonuclease encoded by an intron in the 23 S rRNA gene of the hyperthermophilic archaeon Desulfurococcus mobilis. The structure of I-DmoI has been determined to 2.2 A resolution using multi-wavelength anomalous diffraction techniques. I-DmoI, a protein of the LAGLIDADG motif family, represents the first structure of a freestanding endonuclease with two LAGLIDADG motifs, and the first of a thermostable homing endonuclease. I-DmoI consists of two similar alpha/beta domains (alphabetabetaalphabetabetaalpha) related by pseudo 2-fold symmetry. The LAGLIDADG motifs are located at the carboxy-terminal end of the first alpha-helix of each domain. These helices form a two-helix bundle at the interface between the domains and are perpendicular to a saddle-shaped DNA binding surface, formed by two four-stranded antiparallel beta-sheets. Despite substantially different sequences, the overall fold of I-DmoI is similar to that of two other LAGLIDADG proteins for which the structures are known, I-CreI and the endonuclease domain of PI-SceI. The three structures differ most in the loops connecting the beta-strands, relating to the respective DNA target site sizes and geometries. In addition, the absence of conserved residues surrounding the active site, other than those within the LAGLIDADG motif, is of mechanistic importance. Finally, the carboxy-terminal domain of I-DmoI is smaller and has a more irregular fold than the amino-terminal domain, which is more similar to I-CreI, a symmetric homodimeric endonuclease. This is reversed compared to PI-SceI, where the amino-terminal domain is more similar to carboxy-terminal domain of I-DmoI and to I-CreI, with interesting evolutionary implications.

Crystallization and preliminary crystallographic analysis of the archaeal intron-encoded endonuclease I-DmoI

Two forms of the archaeal intron-encoded site-specific endonuclease I-DmoI, namely I-DmoIc and I-DmoIl, have been purified and crystallized. Crystals of I-DmoIc are rod-shaped and diffract to 3.0 A resolution, but further analysis was hampered by twinning. Crystals of I-DmoIl, which is a six-amino-acid C-terminal truncation of I-DmoIc, are plate shaped and belong to space group C2 with cell parameters a = 93.72, b = 37.03, c = 55.56 A, beta = 113.4 degrees, with one molecule per asymmetric unit (Vm = 2.01 A3 Da-1). The crystals diffract to at least 2.3 A resolution. A complete native data set has been measured and structure determination is on-going.

Intron-encoded endonuclease I-TevII binds across the minor groove and induces two distinct conformational changes in its DNA substrate

I-TevII is the homing endonuclease encoded by the sunY intron of bacteriophage T4. The enzyme cleaves an intronless sunY gene near the exon I-exon II junction, thereby initiating intron homing into its cognate intronless allele. Specifically, I-TevII cleaves its DNA target 13 to 15 nucleotides (nt) downstream of the sunY intron insertion site, generating 2-nl 3'-OH extensions. Here, we present evidence that I-TevII makes predominantly minor groove contacts in two regions of its recognition sequence, as does I-TevI, the other homing endonuclease encoded by phage T4. Following cleavage, I-TevII was shown to remain bound to one of its DNA products, suggesting possible additional roles for the endonuclease in the mobility process. Interestingly, two distinct conformational changes were detected by gel analysis in the DNA substrate following binding by I-TevII, one occurring in the absence of Mg2+, the second being dependent on the presence of Mg2+. The Mg(2+)-induced distortion accompanies a nick in one strand, and may serve to bring the cleavage site on the other strand into proximity with the catalytic domain of the protein.

Crystallization and preliminary crystallographic analysis of two endo-beta-N-acetylglucosaminidases, endo H and endo F1

Endo H and F1 are endoglycosidases that cleave the oligosaccharide moiety of asparagine-linked glycoproteins by hydrolysis of the glycosidic bond in the N,N'-diacetylchitobiose core. The two enzymes are specific for high-mannose oligosaccharides. Here, we report the crystallization and preliminary crystallographic analysis of Endo H and Endo F1. Crystals were grown by hanging drop vapor diffusion methods. Both proteins crystallize from crystallization buffers containing polyethyleneglycol 8000 and zinc acetate as precipitating agents in cacodylate buffer. The crystals of Endo H belong to the tetragonal space group P4(1)2(1)2 (or P4(3)2(1)2) with cell dimensions: a = 85.22 A, c = 89.41 A. The crystals of Endo F1 belong to the hexagonal space group P6(1) (or P6(5)) with cell dimensions: a = 70.61 A, c = 100.32 A. Crystals of both proteins diffract to at least 1.8 A resolution.

The supracloacal chromolipoid body of the black vulture (Coragyps atratus): anatomical, histological and histochemical considerations

During histological and physiological investigations of black vultures (Coragyps atratus) dissection revealed the presence of an "organ", the supracloacal chromolipoid body, which has no counterpart among other warm blooded animals. The organ occurs in both sexes and in birds of different ages. It is located in the median sagittal plane dorsal to the cloaca. It is enveloped by a smooth muscle-connective tissue capsule and has a rich blood supply. The supracloacal body is yellow-brown in color being composed chiefly of islands of pigment cells.Histochemically, the pigment is a chromolipoid as defined by Ciaccio.