Family fingerprints: a global approach to structural classification

Protein domain classification is a useful tool to deduce functional properties of proteins. Many software to classify domains according to available databases have been proposed so far. This paper introduces the notion of "fingerprint" as an easy and readable digest of the similarities between a protein fragment and an entire set of sequences. This concept offers us a rationale for building an automatic SCOP classifier which assigns a query sequence to the most likely family. Fingerprint-based analysis has been implemented in a software tool and we report some experimental validations for it.     

Expression profile of genes associated with mastitis in dairy cattle

In order to characterize the expression of genes associated with immune response mechanisms to mastitis, we quantified the relative expression of the IL-2, IL-4, IL-6, IL-8, IL-10, IFN-γ and TNF- α genes in milk cells of healthy cows and cows with clinical mastitis. Total RNA was extracted from milk cells of six Black and White Holstein (BW) cows and six Gyr cows, including three animals with and three without mastitis per breed. Gene expression was analyzed by real-time PCR. IL-10 gene expression was higher in the group of BW and Gyr cows with mastitis compared to animals free of infection from both breeds (p < 0.05). It was also higher in BW Holstein animals with clinical mastitis (p < 0.001), but it was not significant when Gyr cows with and without mastitis were compared (0.05 < p < 0.10). Among healthy cows, BW Holstein animals tended to present a higher expression of all genes studied, with a significant difference for the IL-2 and IFN- γ genes (p < 0.001). For animals with mastitis no significant difference in gene expression was observed between the two breeds. These findings suggest that animals with mastitis develop a preferentially cell-mediated immune response. Further studies including larger samples are necessary to better characterize the gene expression profile in cows with mastitis.     

Identification of Genes Associated with Local Aggressiveness and Metastatic Behavior in Soft Tissue Tumors

Soft tissue tumors represent a group of neoplasia with different histologic and biological presentations varying from benign, locally confined to very aggressive and metastatic tumors. The molecular mechanisms responsible for such differences are still unknown. The understanding of these molecular alterations mechanism will be critical to discriminate patients who need systemic treatment from those that can be treated only locally and could also guide the development of new drugs'' against this tumors. Using 102 tumor samples representing a large spectrum of these tumors, we performed expression profiling and defined differentially expression genes that are likely to be involved in tumors that are locally aggressive and in tumors with metastatic potential. We described a set of 12 genes (SNRPD3, MEGF9, SPTAN-1, AFAP1L2, ENDOD1, SERPIN5, ZWINTAS, TOP2A, UBE2C, ABCF1, MCM2, and ARL6IP5) showing opposite expression when these two conditions were compared. These genes are mainly related to cell-cell and cell-extracellular matrix interactions and cell proliferation and might represent helpful tools for a more precise classification and diagnosis as well as potential drug targets.     

Redox regulation of cyclophilin A by glutathionylation

Using redox proteomics techniques to characterize the thiol status of proteins in human T lymphocytes, we identified cyclophilin A (CypA) as a specifically oxidized protein early after mitogen activation. CypA is an abundantly expressed cytosolic protein, target of the immunosuppressive drug cyclosporin A (CsA), for which a variety of functions has been described. In this study, we could identify CypA as a protein undergoing glutathionylation in vivo. Using MALDI-MS we identified Cys52 and Cys62 as targets of glutathionylation in T lymphocytes, and, using bioinformatic tools, we defined the reasons for the susceptibility of these residues to the modification. In addition, we found by circular dichroism spectroscopy that glutathionylation has an important impact on the secondary structure of CypA. Finally, we suggest that glutathionylation of CypA may have biological implications and that CypA may play a key role in redox regulation of immunity.     

Evaluation of functional stability of quercetin as a raw material and in different topical formulations by its antilipoperoxidative activity

The present study evaluates the antioxidant activity of the flavonol quercetin, and its functional stability as a raw material and when added in formulations. The iron-chelating activity was determined using the bathophenanthroline assay, and the functional stability was evaluated with the antilipoperoxidative assay. Raw material presented concentration-dependent antilipoperoxidative and iron-chelating activities. The initial antilipoperoxidative activity of the raw material, cream and gel-cream were 63%, 78%, and 69%, respectively. There was no detectable loss of activity during 182 days (6 months) of storage at all tested temperatures (4°C, room temperature [RT], 37°C, and 45°C) for the raw material. Considering the method variability of 10%, activity loss greater than 10% for nonionic cream was detected after 126 days at 4°C (20.1%), decreasing thereafter to 22.2% after 182 days. At 45°C, the loss of activity started after 182 days (13.2%). For the anionic gel-cream, activity loss started after 84 days (28.4%, 45°C), decreasing after 182 days to 40.3% at 45°C. At 37°C, activity loss was detected after 182 days (12%). In conclusion, the results suggest that the activity of quercetin depends on iron chelation, and its posible usefulness as a topical antioxidant to prevent oxidative stress-induced skin damage depends on maintaining its antilipoperoxidative activity stored at RT, which avoids special storage conditions. Published: February 3, 2006     

Skin carotenoid concentration correlates with male hunting skill and territory quality in the kestrel Falco tinnunculus

In the context of sexual selection carotenoid based signals are candidates for indicator traits: they have to be taken up in the diet by animals, they can indicate the ability of the bearer to accumulate a limited resource, and they help in maintaining the health status. We investigated the yellow-orange colouration of the tarsi of the kestrel Falco tinnunculus in relation to sex, diet and to different aspects of male reproductive behaviour. The colouration of the tarsi (estimated as hue) was more intense in males than in females. Among males, the tarsi hue was associated with the intake of invertebrates; this was true also if the population diet was based mainly on voles. Carotenoid based colouration was positively associated with the number of vertebrate preys delivered to the nest per time unit and with territory quality (calculated on the basis of home-range size, habitat extension and prey availability). These results are consistent with predictions derived from good-parent models of sexual selection, suggesting that in the common kestrel carotenoid based colouration is important as an indicator of male quality.     

Upregulation of the novel lncRNA U731166 is associated with migration,invasion and vemurafenib resistance in melanoma

Our previous work using a melanoma progression model composed of melanocytic cells (melanocytes, primary and metastatic melanoma samples) demonstrated various deregulated genes, including a few known lncRNAs. Further analysis was conducted to discover novel lncRNAs associated with melanoma, and candidates were prioritized for their potential association with invasiveness or other metastasis‐related processes. In this sense, we found the intergenic lncRNA {"type":"entrez-nucleotide","attrs":{"text":"U73166","term_id":"1613889","term_text":"U73166"}}U73166 (ENSG00000230454) and decided to explore its effects in melanoma. For that, we silenced the lncRNA {"type":"entrez-nucleotide","attrs":{"text":"U73166","term_id":"1613889","term_text":"U73166"}}U73166 expression using shRNAs in a melanoma cell line. Next, we experimentally investigated its functions and found that migration and invasion had significantly decreased in knockdown cells, indicating an essential association of lncRNA {"type":"entrez-nucleotide","attrs":{"text":"U73166","term_id":"1613889","term_text":"U73166"}}U73166 for cancer processes. Additionally, using naïve and vemurafenib‐resistant cell lines and data from a patient before and after resistance, we found that vemurafenib‐resistant samples had a higher expression of lncRNA {"type":"entrez-nucleotide","attrs":{"text":"U73166","term_id":"1613889","term_text":"U73166"}}U73166. Also, we retrieved data from the literature that indicates lncRNA {"type":"entrez-nucleotide","attrs":{"text":"U73166","term_id":"1613889","term_text":"U73166"}}U73166 may act as a mediator of RNA processing and cell invasion, probably inducing a more aggressive phenotype. Therefore, our results suggest a relevant role of lncRNA {"type":"entrez-nucleotide","attrs":{"text":"U73166","term_id":"1613889","term_text":"U73166"}}U73166 in metastasis development. We also pointed herein the lncRNA {"type":"entrez-nucleotide","attrs":{"text":"U73166","term_id":"1613889","term_text":"U73166"}}U73166 as a new possible biomarker or target to help overcome clinical vemurafenib resistance.     

Phoretic Behaviour of Bromeliad Annelids (<Emphasis Type="Italic">Dero</Emphasis>) and Ostracods (<Emphasis Type="Italic">Elpidium</Emphasis>) using Frogs and Lizards as Dispersal Vectors

The phoretic behaviour of ostracods (Elpidium bromeliarum) andannelids (Dero superterrenus) that inhabit tank bromeliads was studied. Our previous field observations had shown that bromeliad ostracods can be found attached to the skin of amphibians and reptiles that move among bromeliads, probably allowing the ostracods to colonise new tanks. In this paper, we present the first record of bromeliad annelids found attached to frogs moving among bromeliads in the field. We have also enlarged the database on bromeliad ostracods engaged in phoretic association with terrestrial vertebrates in three locations in southeastern Brazil. In our laboratory experiments bromeliad annelids show a strong significant tendency to climb onto papers that had been in contact with frog skin when compared with control papers, indicating a kind of chemically oriented behaviour. Bromeliad ostracods, on the other hand, attached themselves to treated and untreated papers with same frequency. When brought into contact with various species of frogs and lizards, the bromeliad annelids and ostracods both presented preference to attach themselves to frogs, but the annelids showed a stronger preference to attach to frogs and to avoid attachment to lizards. Another experiment demonstrated that bromeliad annelids are much more prone to dehydration than are ostracods. We suggest that the chemically oriented behaviour presented by bromeliad annelids toward frogs could diminish the risk of death by dehydration during the transport among bromeliads due to the moist characteristic of frog skins.     

p21CIP1 is dispensable for the G2 arrest caused by genistein in human melanoma cells

We have investigated the effect of genistein on cell cycle distribution of the human choroidal melanoma cell line OCM-1. We report that this isoflavonoid arrested cells in G2. This effect was correlated with the induction of the CDK inhibitor p21CIP1. However, while CDK1 activity was markedly reduced following genistein treatment, CDK2 activity was not affected. This was in agreement with the absence of G1 arrest that we observed but caused some doubt about the functionality of p21CIP1. Attempts to demonstrate mutation or post-translational modification of p21CIP1 from OCM-1 cells were unsuccessful. In fact, the level of p21CIP1 induced by genistein was shown to be insufficient to cause CDK2 inhibition. The role of p21CIP1 in the inhibition of CDK1 was questionable, as we demonstrated that genistein impaired Tyr15 dephosphorylation of CDK1 and because CDK1-cyclin B1 complexes from treated cells could be reactivated upon exposure to CDC25 phosphatase. Finally, we report that p21CIP1 was not absolutely required for the genistein-induced G2 arrest, as the isoflavone caused at least partial G2 arrest in p21-deficient Rat-1 fibroblasts as well as in p21-/- mouse embryo fibroblasts.