Expression, purification and structural analysis of the Pyrococcus abyssi RNA binding protein PAB1135

Abstract Background The gene coding for the uncharacterized protein PAB1135 in the archaeon Pyrococcus abyssi is in the same operon as the ribonuclease P (RNase P) subunit Rpp30. Findings Here we report the expression, purification and structural analysis of PAB1135. We analyzed the interaction of PAB1135 with RNA and show that it binds efficiently double-stranded RNAs in a non-sequence specific manner. We also performed molecular modeling of the PAB1135 structure using the crystal structure of the protein Af2318 from Archaeoglobus fulgidus (2OGK) as the template. Conclusions Comparison of this model has lead to the identification of a region in PAB1135 that could be involved in recognizing double-stranded RNA.

Clinical, radiographic and histologic analysis of the effects of pulp capping materials used in pulpotomies of human primary teeth

Aim: To compare the clinical, radiographic and histological responses of the pulp to mineral trioxide aggregate (MTA), calcium hydroxide (CH) and Portland cement (PC) when used as a pulpotomy agent in human primary teeth. Study design: Forty-five mandibular primary molar teeth were randomly assigned to CH, MTA or PC groups and treated by pulpotomy technique. Methods: The teeth were treated by conventional pulpotomy technique, differing only in the capping material for each group. Clinical and radiographic evaluations were recorded at 6-, 12- and 24-month follow-up. Teeth in the regular exfoliation period were further processed for histologic analysis. Statistics: The teeth were treated by conventional pulpotomy technique, differing only in the capping material for each group. Clinical and radiographic evaluations were recorded at 6-, 12- and 24-month follow-up. Teeth in the regular exfoliation period were further processed for histologic analysis. Statistics: Clinically and radiographically, the MTA and PC groups showed 100 % success rates at 6, 12 and 24 months. In CH group, several teeth presented clinical and radiographic failures detected throughout the follow-up period, and internal resorption was a frequent radiographic finding. Histologic analysis revealed the presence of dentine-like mineralised material deposition obliterating the root canal in the PC and MTA groups. CH group presented, in most of the sections, necrotic areas in the root canals. Conclusions: MTA and PC may serve as effective materials for pulpotomies of primary teeth as compared to CH. Although our results are very encouraging, further studies and longer follow-up assessments are needed in order to determine the safe clinical indication of Portland cement.

Expression, purification and molecular analysis of the human ZNF706 protein

Background: The ZNF706 gene encodes a protein that belongs to the zinc finger family of proteins and was found to be highly expressed in laryngeal cancer, making the structure and function of ZNF706 worthy of investigation. In this study, we expressed and purified recombinant human ZNF706 that was suitable for structural analysis in Escherichia coli BL21(DH3). Findings: ZNF706 mRNA was extracted from a larynx tissue sample, and cDNA was ligated into a cloning vector using the TOPO method. ZNF706 protein was expressed according to the E. coli expression system procedures and was purified using a nickel-affinity column. The structural qualities of recombinant ZNF706 and quantification alpha, beta sheet, and other structures were obtained by spectroscopy of circular dichroism. ZNF706's structural modeling showed that it is composed of α-helices (28.3%), β-strands (19.4%), and turns (20.9%), in agreement with the spectral data from the dichroism analysis. Conclusions: We used circular dichroism and molecular modeling to examine the structure of ZNF706. The results suggest that human recombinant ZNF706 keeps its secondary structures and is appropriate for functional and structural studies. The method of expressing ZNF706 protein used in this study can be used to direct various functional and structural studies that will contribute to the understanding of its function as well as its relationship with other biological molecules and its putative role in carcinogenesis.

Radiation therapy for Graves' ophthalmopathy: a systematic review and meta-analysis of randomized controlled trials

PURPOSE: To evaluate the efficacy of radiotherapy (RT) with total dose of 20 Gy (RT 20 Gy) in the treatment of Graves' ophthalmopathy. METHODS: A systematic review and meta-analysis of randomized controlled trials was performed comparing RT 20 Gy with or without glucocorticoid to clinical treatments for Graves' ophthalmopathy. The MEDLINE, EMBASE, Cochrane Library databases and recent relevant journals were searched. Relevant reports were reviewed by two reviewers. Response to radiotherapy was defined as clinical success according to each trial. We also evaluated the quality of life and whether RT to produce fewer side effects than other treatments. RESULTS: A total of 8 randomized controlled trials (439 patients) were identified. In the subgroup analysis, the overall response to treatment rates was better for: RT 20 Gy plus glucocorticoid vs glucocorticoids alone, OR=17.5 (CI95% 1.85-250, p=0.04), RT 20 Gy vs sham RT, OR= 3.15 (CI95%1.59-6.23, p=0.003) and RT 20Gy plus intravenous glucocorticoid vs RT 20Gy plus oral glucocorticoid, OR=4.15(CI95% 1.34-12.87, p=0.01). There were no differences between RT 20 Gy versus other fractionations and RT 20 Gy versus glucocorticoid alone. RT 20 Gy with or without glucocorticoids showed an improvement in diplopia grade, visual acuity, optic neuropathy, lid width, proptosis and ocular motility. No difference was seen for costs, intraocular pressure and quality of life. CONCLUSION: Our data have shown that RT 20 Gy should be offered as a valid therapeutic option to patients with moderate to severe ophthalmopathy. The effectiveness of orbital radiotherapy can be increased by the synergistic interaction with glucocorticoids. Moreover, RT 20 Gy is useful to improve a lot of ocular symptoms, excluding intraocular pressure, without any difference in quality of life and costs.

Nitric oxide plasma/serum levels in patients with schizophrenia: a systematic review and meta-analysis

For the last 40 years, schizophrenia has been considered to be the result primarily of a dysfunction in brain dopaminergic pathways. In this review, it is described and discussed findings concerning nitric oxide-mediated neurotransmission in schizophrenia. Studies were searched in PubMed, SciELO, and LILACS using the terms schizophrenia and nitric oxide plasma levels or nitric oxide serum levels, with no time limit. The reference lists of selected articles were also hand-searched for additional articles. From 15 potential reports, 10 were eligible to be included in the review and meta-analysis. These studies included a total of 505 patients with schizophrenia and 339 healthy volunteers. No significant difference was found between patients and healthy controls regarding total nitrite plasma/serum levels (effect size g = 0.285, 95%CI = -0.205 to 0.774, p = 0.254). However, when studies with patients under antipsychotic treatment were examined separately, there was a significant difference between patients and healthy volunteers (effect size g = 0.663, 95%CI = 0.365 to 0.961, p < 0.001), showing that patients under treatment have higher levels of plasma/serum nitric oxide than controls. These results suggest that antipsychotics increase nitric oxide plasma/serum levels and that the nitrergic pathway would be a fertile target for the development of new treatments for patients with schizophrenia.

Experimental and numerical analysis of dry contact in the pin on disc test

The reduction of friction and wear in systems presenting metal-to-metal contacts, as in several mechanical components, represents a traditional challenge in tribology. In this context, this work presents a computational study based on the linear Archard's wear law and finite element modeling (FEM), in order to analyze unlubricated sliding wear observed in typical pin on disc tests. Such modeling was developed using finite element software Abaqus® with 3-D deformable geometries and elastic–plastic material behavior for the contact surfaces. Archard's wear model was implemented into a FORTRAN user subroutine (UMESHMOTION) in order to describe sliding wear. Modeling of debris and oxide formation mechanisms was taken into account by the use of a global wear coefficient obtained from experimental measurements. Such implementation considers an incremental computation for surface wear based on the nodal displacements by means of adaptive mesh tools that rearrange local nodal positions. In this way, the worn track was obtained and new surface profile is integrated for mass loss assessments. This work also presents experimental pin on disc tests with AISI 4140 pins on rotating AISI H13 discs with normal loads of 10, 35, 70 and 140 N, which represent, respectively, mild, transition and severe wear regimes, at sliding speed of 0.1 m/s. Numerical and experimental results were compared in terms of wear rate and friction coefficient. Furthermore, in the numerical simulation the stress field distribution and changes in the surface profile across the worn track of the disc were analyzed. The applied numerical formulation has shown to be more appropriate to predict mild wear regime than severe regime, especially due to the shorter running-in period observed in lower loads that characterizes this kind of regime.

Lithogenic flux and textural analysis of the sediment trap samples collected at 150m in the Canary basin, Spain

Trabajo Finde Título para obtener el Grado en Ciencia del Mar

Diencephalic asymmetries: morphological, immunohistochemical and ultrastructural analysis of habenular nuclei in elasmobranchs and teleosts

The habenular nuclei are diencephalic structures present in Vertebrates and they form, with the associated fiber systems, a part of the system that connects the telencephalon to the ventral mesencephalon (Concha M. L. and Wilson S. W., 2001). In representative species of almost all classes of Vertebrates the habenular nuclei are asymmetric, both in terms of size and of neuronal and neurochemical organization, although different types of asymmetry follow different evolutionary courses. Previous studies have analyzed the spread and diversity of the asymmetry in species for which data are not clear (Kemali M. et al., 1980). Notwithstanding that, it’s still not totally understood the evolution of the phenomenon, and the ontogenetic mechanisms that have led to the habenular asymmetry development are not clear (Smeets W.J. et al., 1983). For the present study 14 species of Elasmobranchs and 15 species of Teleostean have been used. Brains removed from the animals have been fixed using 4% paraformaldehyde in phosphate buffer; brains have been analyzed with different tecniques, and I used histological, immunohistochemical and ultrastructural analysis to describe this asymmetry. My results confirm data previously obtained studying other Elasmobranchs species, in which the left habenula is larger than the right one; the Teleostean show some slightly differences regarding the size of the habenular ganglia, in some species, in which the left habenular nucleus is larger than the right. In the course of studies, a correlation between the habits of life and the diencephalic asymmetry seems to emerge: among the Teleostean analyzed, the species with benthic life (like Lepidorhombus boscii, Platichthys flesus, Solea vulgaris) seem to possess a slight asymmetry, analogous to the one of the Elasmobranchs, while in the other species (like Liza aurata, Anguilla anguilla, Trisopterus minutus) the habenulae are symmetrical. However, various aspects of the neuroanatomical asymmetries of the epithalamus have not been deepened in order to obtain a complete picture of the evolution of this phenomenon, and new searches are needed to examine the species without clear asymmetry, in order to understand the spread and the diversity of the asymmetry among the habenulae between the Vertebrates.

Mechanism of colonization in the Mediterranean-sea. Asperarca nodulosa: morphological and genetic analysis

Il mar Mediterraneo è un bacino acquifero peculiare per la recente colonizzazione di specie aliene, per l’evento geologico legato alla Crisi di salinità del Messiniano e per l’ampio range di salinità. L’individuazione dei meccanismi di colonizzazione si è incentrata sullo studio morfologico, istologico e molecolare delle specie Asperarca nodulosa ed Anadara demiri (Arcidae-Bivalvia-Mollusca). La ricerca si è basata sulla caratterizzazione morfologica, con utilizzo del microscopio elettronico a scansione, al fine di individuare il tipo di sviluppo larvale. Successivamente i dati rilevati al S.E.M. sono stati supportati dall’indagine istologica che ha evidenziato la presenza di gonadi a sessi distinti e la non incubazione larvale. L’ulteriore analisi filogenetica ha permesso di evidenziare la netta suddivisione tra le tre popolazioni studiate, indagine effettuata tramite marcatori arbitrari (RAPDs) e nucleari specifici (ITS). I risultati ottenuti trovano supporto da quanto noto su base morfologica. I dati, nel complesso, mostrano una perdita delle capacità di diffusione della specie tramite sviluppo larvale plantotrofico a favore di quello lecitotrofico o diretto; tale tesi è ulteriormente supportata dai dati molecolari che mostrano una netta separazione delle popolazioni prese in esame ed un conseguente isolamento tra individui appartenenti a zone di profondità del Mediterraneo (sub-bacini abissali). La ricerca ha, inoltre,esaminato i meccanismi di introduzione attuali nel bacino acquifero che è soggetto ad una nuova invasione da parte specie aliene dovuta all’apertura del canale di Suez. L’analisi si è focalizzata sullo studio per l’ individuazione dell’origine della specie aliena A. demiri , di presunta derivazione Indo-Pacifica, ma rivelatasi, nei dati preliminari, di origine Atlantica.

The meccano method for finite element and isogeometric analysis

Congresos y conferencias

Mesh Generation and Isogeometric Analysis

[EN]We present advances of the meccano method [1,2] for tetrahedral mesh generation and volumetric parameterization of solids. The method combines several former procedures: a mapping from the meccano boundary to the solid surface, a 3-D local refinement algorithm and a simultaneous mesh untangling and smoothing. The key of the method lies in defining a one-to-one volumetric transformation between the parametric and physical domains. Results with adaptive finite elements will be shown for several engineering problems. In addition, the application of the method to T-spline modelling and isogeometric analysis [3,4] of complex geometries will be introduced…