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We apply a simulational proxy of the [lowercase_phi_synonym]-value analysis and perform extensive mutagenesis experiments to identify the nucleating residues in the folding “reactions” of two small lattice Gō polymers with different native geometries. Our findings show that for the more complex native fold (i.e., the one that is rich in nonlocal, long-range bonds), mutation of the residues that form the folding nucleus leads to a considerably larger increase in the folding time than the corresponding mutations in the geometry that is predominantly local. These results are compared to data obtained from an accurate analysis based on the reaction coordinate folding probability Pfold and on structural clustering methods. Our study reveals a complex picture of the transition state ensemble. For both protein models, the transition state ensemble is rather heterogeneous and splits up into structurally different populations. For the more complex geometry the identified subpopulations are actually structurally disjoint. For the less complex native geometry we found a broad transition state with microscopic heterogeneity. These findings suggest that the existence of multiple transition state structures may be linked to the geometric complexity of the native fold. For both geometries, the identification of the folding nucleus via the Pfold analysis agrees with the identification of the folding nucleus carried out with the [lowercase_phi_synonym]-value analysis. For the most complex geometry, however, the applied methodologies give more consistent results than for the more local geometry. The study of the transition state structure reveals that the nucleus residues are not necessarily fully native in the transition state. Indeed, it is only for the more complex geometry that two of the five critical residues show a considerably high probability of having all its native bonds formed in the transition state. Therefore, one concludes that, in general, the [lowercase_phi_synonym]-value correlates with the acceleration/deceleration of folding induced by mutation, rather than with the degree of nativeness of the transition state, and that the “traditional” interpretation of [lowercase_phi_synonym]-values may provide a more realistic picture of the structure of the transition state only for more complex native geometries. [ABSTRACT FROM AUTHOR]

This study evaluated the prognosis factors of age, tumour size, anatomic location, histological grade and proliferating cell nuclear antigen ( PCNA) expression in 13 dogs with oral squamous cell carcinoma ( OSCC) with bone invasion and without signs of lymph node or distant metastasis. All animals were treated with radical excision performed with at least 1 cm margin, based on computed tomography images. In the 2-year follow-up, median disease-free survival was 138 days for dogs with grade 3 tumours and was not reached for those with grade 2 tumours. Grade 3 tumours and PCNA labelling index ≥65% were related with a shorter disease-free survival time and consequently poor prognosis ( p = 0.003 and p = 0.034, respectively). Mean PCNA labelling index was significantly higher in recurrent cases ( p = 0.011). Histological grade and PCNA expression may be important prognosis factors in canine OSCC. [ABSTRACT FROM AUTHOR]

Marine turtle fibropapillomatosis is an emerging disease that affects marine turtles worldwide. This report describes the histopathological features and involvement of chelonid fibropapilloma-associated herpesvirus in marine turtle fibropapillomatosis detected in the green turtle Chelonia mydas at Príncipe Island, Gulf of Guinea. The histopathological findings confirmed the presence of fibropapillomas with both verrucous and fibromatous subtypes. Quantitative real-time PCR was used for detection of chelonid fibropapilloma-associated herpesvirus in tissue samples (n = 18) collected from afflicted (n = 10) and apparently healthy turtles (n = 2), revealing 94.4% positive samples, confirming the presence of viral sequences not only in fibropapillomatosis lesions but also in the skin of apparently healthy animals. [ABSTRACT FROM AUTHOR]

Onchocercosis is a newly recognized disease in dogs that has been reported with higher frequency in Europe and in the United States. We report a case of a 3-year-old male mongrel stray dog from the Algarve region (South Portugal) who had a retrobulbar granuloma containing a filaroid nematode of the genus Onchocerca. A gravid adult female parasite was embedded in a granulomatous inflammation adjacent to the sclera beyond the retina. The parasite was 191 to 267 μm in diameter (mean = 225 μm), surrounded by a cuticule and owing a uterus that was filled with small unsheated microfilariae. The cuticule consisted of two separated layers in longitudinal sections. The external layer had cuticular ridges and the internal layer contained striations. Sequencing of the COI and ND5 mitochondrial genes confirmed the identity of this parasite as Onchocerca lupi. Furthermore, the first sequence of the 12S mitochondrial gene is reported in this study. [ABSTRACT FROM AUTHOR]

Biologically speaking, Sendai virus (SeV), the murine parainfluenza virus type 1, is perceived as a common respiratory pathogen that is endemic in many rodent colonies throughout the world. Currently it is believed that SeV is the leading cause of pneumonia in mice and together with the mouse hepatitis viruses, is the most prevalent and important of the naturally occurring infections of mice. The scientific community also considers SeV as the archetype organism of the Paramyxoviridae family because most of the basic biochemical, molecular and biologic properties of the whole family were derived from its own characteristics. Recently, scientific interest for this old pathogen has re-emerged, this time because of its potential value as a vector for gene transfer. This review aimed at drawing an exhaustive picture of this multifaceted pathogen. [ABSTRACT FROM AUTHOR]

Here we describe the establishment of a new canine mammary tumour ( CMT) cell line, FR37-CMT that does not show dependence on female hormonal signaling to induce tumour xenografts in NOD-SCID mice. FR37-CMT cell line has a stellate or fusiform shape, displays the ability to reorganize the collagen matrix, expresses vimentin, CD44 and shows the loss of E-cadherin which is considered a fundamental event in epithelial to mesenchymal transition ( EMT). The up-regulation of ZEB1, the detection of phosphorylated ERK1/2 and the downregulation of DICER1 and miR-200c are also in accordance with the mesenchymal characteristics of FR37-CMT cell line. FR37-CMT shows a higher resistance to cisplatin ( IC50>50 µM) and to doxorubicin ( IC50>5.3 µM) compared with other CMT cell lines. These results support the use of FR37-CMT as a new CMT model that may assist the understanding of the molecular mechanisms underlying EMT, CMT drug resistance, fostering the development of novel therapies targeting CMT. [ABSTRACT FROM AUTHOR]

Gō models are exceedingly popular tools in computer simulations of protein folding. These models are native-centric, i.e., they are directly constructed from the protein's native structure. Therefore, it is important to understand up to which extent the atomistic details of the native structure dictate the folding behavior exhibited by Gō models. Here we address this challenge by performing exhaustive discrete molecular dynamics simulations of a Gō potential combined with a full atomistic protein representation. In particular, we investigate the robustness of this particular type of Gō models in predicting the existence of intermediate states in protein folding. We focus on the N47G mutational form of the Spc-SH3 folding domain (x-ray structure) and compare its folding pathway with that of alternative native structures produced in silico. Our methodological strategy comprises equilibrium folding simulations, structural clustering, and principal component analysis. [ABSTRACT FROM AUTHOR]