Top PDF Prediction of P53 mutants (multiple sites) transcriptional activity based on structural (2D&3D) properties.

Prediction of P53 mutants (multiple sites) transcriptional activity based on structural (2D&3D) properties.

Prediction of P53 mutants (multiple sites) transcriptional activity based on structural (2D&3D) properties.

This research was dedicated to formulating novel computational approaches to predict and classify the transcriptional activity of multiple site (one-site, two-site, three-site, four-site, and five-site) p53 mutants using optimal set of predictive features that generated higher MCC and accuracy in prediction compared to previous work. Our method placed emphasis on the 2D structure surface of the p53 mutants and the 3D structural changes of the tumor protein, that have been reported to be highly essential in deciding the p53 activity [20–21][25]. In this work we introduced three novel predictor methods. The first method targeted the detection of single independent p53 mutation activity while the second and third approaches were found suitable to predict the activity of co- occurring mutations that combined with the one-site p53 mutants. The second approach generated higher MCC in prediction with both a very large/small number of instances and imbalanced class distribution of records while the third approach served well with fewer instances and balanced records. To maintain brevity, we will call the first, second and third approaches as Independent Predictor (IP), Imbalanced Mutation Predictor (IMP) and Balanced Predictor (BP) methods respectively. We utilized the feature sets obtained by the CFS Subset Evaluator commonly for all the approaches. The features extracted by this technique were passed in an incremental manner to the classifiers to determine the prediction accuracy. Three benchmark classification algorithms viz, Bayesian Network Learning algorithm and Ensemble classi- fiers viz, AdaBoost Learning using Decision Stump (ABDS) algorithm and Random Committee using Random Tree (RCRT) algorithm showed improved results in prediction. The perfor- mance of the classifiers was evaluated using Jack-knife cross- validation technique based on the following scores: Mathews Correlation Coefficient ( < MCC ), Accuracy ( < ACC ), Sensitivity
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Prediction of cancer cell sensitivity to natural products based on genomic and chemical properties

Prediction of cancer cell sensitivity to natural products based on genomic and chemical properties

Curcumin, a phenolic compound from the rhizome of the plant Curcuma longa, induced apoptosis in tumor cells via a p53-dependent pathway or pathways independent of p53. We predicted responses of 7 cell lines that are sensitive to Curcumin, including 4 cell lines from melanoma, 1 cell line from lung cancer, 1 cell line from breast cancer, and 1 cell line from pancreatic cancer (Table S5). Notably, of the 7 cell lines that were defined as responders, 6 were correctly classified by our model (Table 2). The only cell line that was classified incorrectly is Sk-mel-5, a melanoma cell line containing wild-type p53. Because the rest 3 melanoma cell lines in this study contain mutant p53 (Bush et al., 2001), this may explain why our method could not obtain the correct result in Sk-mel-5 cell line.
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Comparison of effects of p53 null and gain-of-function mutations on salivary tumors in MMTV-Hras transgenic mice.

Comparison of effects of p53 null and gain-of-function mutations on salivary tumors in MMTV-Hras transgenic mice.

Several mechanisms have been proposed for the gain-of-function activities of mutant p53 [38]. One of these mechanisms proposes that mutant p53 actively regulates a unique set of genes, the activities of which endow the cell with a growth advantage, chemoresistance, altered metabolism and other properties [38]. Unlike wild-type p53, which depends on its sequence- specific DNA binding for its transactivation activity, genes regulated by mutant p53 lack a con- sensus DNA binding site in their promoter regions [38]. It has thus been proposed that instead of binding to a common response sequence, mutant p53 preferentially binds to stereo-specific DNA configurations [55,56]. Alternatively, mutant p53 may bind to target genes indirectly, i.e. by interactions with other transcription factors, e.g. Sp1 [57,58], Ets [59], NF-Y [21], VDR [60] and SREBP [35]. Although these findings support a transcription-dependent mechanism for the gain-of-function activities of mutant p53, this hasn’t been tested strictly in an in vivo setting or under physiological conditions. Rather, most of the observations have been made by over- expressing mutant p53 in p53-null cells, and in many cases, in the presence of stress signals. Additionally, almost all of the previous studies only utilized a comparison between cells with- out p53 and those expressing mutant p53, a study design lacking the ability to detect any resid- ual wild-type function of the mutants.
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Cheating by exploitation of developmental prestalk patterning in Dictyostelium discoideum.

Cheating by exploitation of developmental prestalk patterning in Dictyostelium discoideum.

The cooperative developmental system of the social amoeba Dictyostelium discoideum is susceptible to exploitation by cheaters—strains that make more than their fair share of spores in chimerae. Laboratory screens in Dictyostelium have shown that the genetic potential for facultative cheating is high, and field surveys have shown that cheaters are abundant in nature, but the cheating mechanisms are largely unknown. Here we describe cheater C (chtC), a strong facultative cheater mutant that cheats by affecting prestalk differentiation. The chtC gene is developmentally regulated and its mRNA becomes stalk-enriched at the end of development. chtC mutants are defective in maintaining the prestalk cell fate as some of their prestalk cells transdifferentiate into prespore cells, but that defect does not affect gross developmental morphology or sporulation efficiency. In chimerae between wild-type and chtC mutant cells, the wild-type cells preferentially give rise to prestalk cells, and the chtC mutants increase their representation in the spore mass. Mixing chtC mutants with other cell- type proportioning mutants revealed that the cheating is directly related to the prestalk-differentiation propensity of the victim. These findings illustrate that a cheater can victimize cooperative strains by exploiting an established developmental pathway.
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Spatial prediction of soil properties in two contrasting physiographic regions in Brazil

Spatial prediction of soil properties in two contrasting physiographic regions in Brazil

ABSTRACT: This study compared the performance of ordinary kriging (OK) and regression krig- ing (RK) to predict soil physical-chemical properties in topsoil (0-15 cm). Mean prediction of error and root mean square of prediction error were used to assess the prediction methods. Two watersheds with contrasting soil-landscape features were studied, for which the prediction methods were performed differently. A multiple linear stepwise regression model was performed with RK using digital terrain models (DTMs) and remote sensing images in order to choose the best auxiliary covariates. Different pedogenic factors and land uses control soil property distribu- tions in each watershed, and soil properties often display contrasting scales of variability. Envi- ronmental covariables and predictive methods can be useful in one site study, but inappropriate in another one. A better linear correlation was found at Lavrinha Creek Watershed, suggesting a relationship between contemporaneous landforms and soil properties, and RK outperformed OK. In most cases, RK did not outperform OK at the Marcela Creek Watershed due to lack of linear correlation between covariates and soil properties. Since alternatives of simple OK have been sought, other prediction methods should also be tested, considering not only the linear relation- ships between covariate and soil properties, but also the systematic pattern of soil property distributions over that landscape.
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Adaptive Neuro-Fuzzy Inference System Applied QSAR with Quantum Chemical Descriptors for Predicting Radical Scavenging Activities of Carotenoids.

Adaptive Neuro-Fuzzy Inference System Applied QSAR with Quantum Chemical Descriptors for Predicting Radical Scavenging Activities of Carotenoids.

This result postulates that antioxidant activities of carotenoids were mainly contributed by both of the neutral and cationic carotenoid molecules rather than either of them. Since the chemical potential (negative electronegativity) is a thermodynamic property derived by differ- entiating the energy with respect to the number of electrons [25], it indicates the direction of chemical reactions as a partial free energy. Thus, a positive relationship was observed between the chemical potential and the TEAC. The postulated mechanism of radical scavenging activi- ties of carotenoids with limited information from correlation analysis is related with the sequential donation of two electrons to radical species. Chemical potential, μ, as a driving force for electron transfer [25] is responsible for first electron transfer reaction and μ cat is responsible
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Carlos Luís de Oliveira Macedo Serra

Carlos Luís de Oliveira Macedo Serra

The work of Roelfstra et al. (1985) from 1985 shows the advantages of using finite element models to describe the different phenomena occurring inside the concrete during hardening, focusing on the deformation properties, such as elasticity and shrinkage. Prac- tical mesoscopic applications for the prediction of concrete behaviour or for the study of a specific effect or property using continuum models are presented by Carol et al. (2001) and Wang et al. (2016), in which interface elements in a finite element mesh define the fracture behaviour at the ITZ. The work of Benboudjema et al. (2004), Xotta et al. (2013), and Havlásek and Jirásek (2015), consider the creep properties, the behaviour of ITZ, the effect of drying and a damage model coupled with softening plasticity (Benboudjema et al. 2004). Both examples show the importance of the ITZ behaviour on the properties of concrete and the effect of local damage on the development of the cracking patterns and, ultimately on the failure mode. The work of Wriggers and Moftah (2006) focuses on the effective properties of concrete and shows the agreement between experimental results, composite and numerical model results considering the aggregate size distribution. The representation of the mesostructure of concrete allows for a more detailed research of specific studies, such as the coupling between creep and damage in which the physical explanation takes place at the mesoscale (Saliba et al. 2012), the development of internal self-balanced stresses that occur during hydration and hardening of concrete (Briffaut et al. 2013; Xu et al. 2017) and the study of stress development on concrete with alkali-silica reactions (Giorla et al. 2015). It is known that stiff aggregates restrain the deformations, introduces a non-uniform stress field inside concrete in which there are highly stressed areas and that creep has a significant role in the relaxation of these stresses (Briffaut et al. 2013; Giorla et al. 2015).
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MATERIAL AND METHODS Study area

MATERIAL AND METHODS Study area

The importance of clay mineralogy for the maintenance of the soil physical quality has been recognized for a long time, especially in soils with low organic matter content, which are typical of tropical regions (Six et al., 2002; Duiker et al., 2003; Igwe et al., 2009; McBride et al., 2012). In fact, a number of early studies report a favorable effect of iron (Fe) oxides on the clay fraction and on the soil physical properties (Lutz, 1936; Kroth & Page, 1947; Chesters et al., 1957; Blackmore, 1973; Schwertmann & Kämpf, 1985; Igwe et al., 1995, 2009; Camargo et al., 2008b), but some reported no such effect (Desphande et al., 1968; Borggaard, 1983). According to Duiker et al. (2003), the absence of correlation between the Fe oxyhydroxides contents and soil aggregation may result from the weaker influence of these contents than of crystallinity. Thus, according to Azevedo & Bonumá (2004), poorly crystalline oxides act as cementing agents facilitating soil aggregation. Anda et al. (2008) and Camargo et al. (2008a) also found that low crystallinity of clay minerals in Oxisols had a positive impact on soil aggregation.
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Stability of p53 homologs.

Stability of p53 homologs.

smaller amplitude than for the full-length protein. The slope of the Arrhenius plot (Figures 1B and S2) was similar for both unfolding events, suggesting similar activation energies. A possible explana- tion for these observations is that the acidic N-terminus of p53 interacts transiently and unspecifically with the basic DBD and C- terminal domains of other p53 molecules [22]. As the concentra- tion of protein in these experiments (15–60 m M) was much higher than the dissociation constant of the p53 tetramer (ca. 20 nM) [30], such interactions are likely to involve different tetramers. It remains to be seen if this observation has physiological relevance. Additionally, the precipitation of protein aggregates, charac- terised by a drop in fluorescence intensity, depended on the p53 construct used. Earlier studies have shown that the p53DBD readily aggregates under different denaturing conditions, thereby making the process of denaturation irreversible [10,18,28,31,32]. Here, aggregation occurred earlier for constructs without the N- terminal domain (QM-Hsp53DBD, QM-Hsp53CT and QM- Hsp53CTC), but was not detected within the time frame examined for QM-p53NCT and full-length p53 (Hsp53 and QM-Hsp53, Figure 2B). This suggests that the N-terminal domain is also important in preventing p53 aggregation.
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Mechanical properties of investment casting moulds reinforced with ceramic fibre

Mechanical properties of investment casting moulds reinforced with ceramic fibre

It should be emphasized that all the examined grain-fibre materials have been characterised by high bending strength MOR1 and all of them have reached the level of minimum material strength during dewaxing of 2.4 MPa, as demanded by American regulations. However, in order to avoid the shell cracking during pattern burning off process, a trend occurs to achieve higher values of MOR1 index, over 4.5 MPa if possible. This condition has been satisfied by a majority of slurries produced according to the experimental design, what confirms that optimum levels of component fractions have been taken into account.
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Structure and stability insights into tumour suppressor p53 evolutionary related proteins.

Structure and stability insights into tumour suppressor p53 evolutionary related proteins.

The p53 family of genes and their protein products, namely, p53, p63 and p73, have over one billion years of evolutionary history. Advances in computational biology and genomics are enabling studies of the complexities of the molecular evolution of p53 protein family to decipher the underpinnings of key biological conditions spanning from cancer through to various metabolic and developmental disorders and facilitate the design of personalised medicines. However, a complete understanding of the inherent nature of the thermodynamic and structural stability of the p53 protein family is still lacking. This is due, to a degree, to the lack of comprehensive structural information for a large number of homologous proteins and to an incomplete knowledge of the intrinsic factors responsible for their stability and how these might influence function. Here we investigate the thermal stability, secondary structure and folding properties of the DNA-binding domains (DBDs) of a range of proteins from the p53 family using biophysical methods. While the N- and the C-terminal domains of the p53 family show sequence diversity and are normally targets for post- translational modifications and alternative splicing, the central DBD is highly conserved. Together with data obtained from Molecular Dynamics simulations in solution and with structure based homology modelling, our results provide further insights into the molecular properties of evolutionary related p53 proteins. We identify some marked structural differences within the p53 family, which could account for the divergence in biological functions as well as the subtleties manifested in the oligomerization properties of this family.
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A correlação da expressão do gene p53 no carcinoma invasor de colo uterino com fatores clínicos e prognóstico

A correlação da expressão do gene p53 no carcinoma invasor de colo uterino com fatores clínicos e prognóstico

O p53 foi negativo em 10,8% dos casos segundo a literatura da imunohistoquimica pode indicar estado de p53 tipo selvagem (ou seja, p53 com função normal) ou p53 inativado resultando da[r]

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α-Calcium calmodulin kinase II modulates the temporal structure of hippocampal bursting patterns.

α-Calcium calmodulin kinase II modulates the temporal structure of hippocampal bursting patterns.

We saw that the percent of variance in pixel-by-pixel firing rate explained by regression on position was lower for T305D mice compared to WT mice (Firing rate percent variance explained for T305D = 60.3% vs. WT = 67.7%, p,0.001). In other words, having access to the animal’s position was less useful in predicting place cell firing rate for T305D mutants. This result is not very surprising, since spatial coherence for T305D mice was also lower. Spatial coherence measures the correlation in firing rate between a position pixel and the neighboring 8 pixels around it, over the whole area. The spatial regression utilized here differs from spatial coherence, since the data fit utilizes firing information over a larger number of pixels in the neighborhood of each pixel to predict its firing rate. The neighborhood size could potentially include the whole area, if necessary. We also adapt the neighborhood size for each cell, and fit using a neighborhood size through a smoothing parameter that yields the best results, as described in the next parameter. We think the spatial regression utilized here is a better estimate of inter-dependence of local firing rate of place cells than spatial coherence, since it is not dependent on pixel sizes but on the smoothness of the firing rate place field. We now discuss the choice of spatial smoothing parameter. One of the shortcomings of spatial coherence or spatial information measures is that they are closely dependent on the size of each position pixel. Larger pixels would smooth the place field more, and result in higher spatial coherence or lower spatial information. Too small a pixel size on the other hand would result in lower spatial coherence or higher spatial information. Rather than comparing firing rate correlation between a pixel and its surrounding (i.e., spatial coherence) or departure in the distribu- tion from uniform firing rate (i.e., spatial information), we asked what is the best prediction job one can do using available place dependent firing rate information irrespective of the extent of spatial neighborhood used for the prediction. With this thought, we think the simplest plausible method was to use a spatial regression with a smoothing parameter individually tuned to each place cell.
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Keratoconus prediction using a finite element model of the cornea with local biomechanical properties

Keratoconus prediction using a finite element model of the cornea with local biomechanical properties

Although many types of refractive surgeries have been modeled using these sophisticated FE methods, little atten- tion has been given to the study of keratoconus using these same techniques. To our knowledge, there is no biomecha- nical model available that satisfactorily explains the arising, the stability or the evolution of keratoconus. That is, which keratoconus is and will remain incipient, which cases will progress and become critical, and so forth. When cases are difficult and there is chance of ambiguity, it is not uncommon for the eye-care professional to examine close relatives of patients in order to accomplish a more precise diagnosis. Patients with keratoconus are usually unhappy with spec- tacle corrections due to the manifestation of higher order aberrations (20-21) , which are mostly consequence of anterior
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Biochemical and histological characterization of tomato mutants

Biochemical and histological characterization of tomato mutants

In this paper we have reported biochemical and histological alterations in tomato mutants. The results provide new insight into the base of the photomorphogenic, hormonal and developmental mutations. Although now the use of new molecular and genomics tools have provided useful information about the developmental control, our results through the use of simple mutants have raised interesting questions about the factors that control the oxidant and antioxidant signalling as well as roots and leaves anatomy. However, while the factors that we have approached might shed light on the regulation of biochemical and anatomical mechanisms, we are now exploring other tomato mutants through the molecular and physiological approaches involving jasmonic acid insensitive, brassinosteroid insensitive or defective, gibberellin defective or constitutive gebberellin response and cryptochrome deicient. Moreover, doubles and multiples mutants, besides those mutants in this current work, will provide for the elucidation of a wide range of complex responses
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The novel fusion proteins, GnRH-p53 and GnRHIII-p53, expression and their anti-tumor effect.

The novel fusion proteins, GnRH-p53 and GnRHIII-p53, expression and their anti-tumor effect.

To assess the permeability across membranes of p53 fusion proteins, H1299 cells incubated with p53, GnRH-p53 and GnRH III-p53 (40 μg/ml) or PBS for 4h were analyzed by immunofluorescence. Samples were blocked with 10% goat serum for 30 min at room temperature. The cells were incubated with monoclonal antibody DO-1 and rabbit against human GnRHR polyconal antibody (Boster CO., LTD. Wuhan) at 4 °C overnight. TRITC-Conjugated AffiniPure Goat Anti- mouse IgG and FITC-Conjugated AffiniPure Goat Anti- rabbit IgG (Zhongshan Golden Bridge CO., LTD. Beijing) were used as second antibodies and added into six-well culture plates at 37°C for 1h. After washing for 5 times with cold PBS, the cells in wells were incubated with Hoechst 33342 at room temperature for 10 minutes in order to dye the cell nuclei. Cells were washed with PBS for 5 min three times and viewed with a fluorescence microscope.
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Construction of the mutants by PCR mutagenesis

Construction of the mutants by PCR mutagenesis

In the common bean (Phaseolus vulgaris), α-AI exist as at least two allelic variants that differ in their specificity towards α-amylases, despite their high degree of similarity (78% amino acid sequence identity). Alfa- amylase inhibitor-1 (α-AI1) is the isoform found in cultivated beans (Moreno & Chrispeels, 1989) and inhibits porcine pancreatic α-amylase (PPA), as well as the α-amylases of the cowpea weevil Callosobruchus maculatus (CMA) and the azuki bean weevil (Callosobruchus chinensis) (Kasahara et al., 1996), but not the amylase of bruchid (Zabrotes subfasciatus) (ZSA) (Ishimoto & Kitamura, 1989). Alpha-amylase inhibitor-2 (α-AI2) is found in some wild bean accessions (Suzuki et al., 1993) and, in contrast, only inhibits ZSA. The growth of larvae of two seed feeding beetles, C. maculates and C. chinensis, is inhibited when the diet of the larvae contains relatively low levels of common bean α-AI (Ishimoto & Kitamura, 1989). Pea transgenic seeds containing up to 0.1%–1.2% of α-AI1 were resistant to cowpea weevils and azuki bean weevils (Shade et al., 1994). Furthermore, in field trials, peas expressing α-AI1 were protected against damage by the pea weevil (Pusztai et al., 1999), suggesting that gene transfer mechanism can be used to make legumes resistant to bruchids. Common beans resistant to Z. subfasciatus have already been produced by traditional breeding techniques but presently there are no inhibitors in beans that are effective against Acanthoscelides obtectus, another important storage bean insect pest. A better understanding of the molecular basis of specificity of α-AI and their target amylases therefore has potential practical benefits.
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Sao Paulo Med. J.  vol.115 número1

Sao Paulo Med. J. vol.115 número1

B rachlnan et aI.2 investigated 31 specir11ens of head and neck EC s and observed rnutations of gene p53 in 53 percent of cases, dem onstrated by polY lnorphisll1 of single strand confon11ation. The salne investigators later detecteel m utations in gene p53 by the polY lnerase chain re£1ction in 63 percent of the cell lines studied. O f the 3 I cases of head and neck EC s studied by C hung et £11.,72 I presenteei at least one m utation of gene p53, analyzed by the single chain polym orphisl11 confon11ation l11ethod. Field et aI.,1O in a study of73 EC s cases, observed the presence of protein p 5 3 o ver e x p r e s s i o n i n 67 p e r c e n t o f t h e In b y im m unohistochem istry. In another il11l11unohistochelnical study, Frank et aI.I3 detected p53 overexpression in 37 percent of cases of EC s of the hypopharynx. Shin et £11.32 obtained a 43 percent index in an il11111unohistocheI11ic£11 study of head and neck EC s. The presence of p53+ in 48 percent of the 63 head and neck EC s cases positive for p53 in our study is com patible w ith literature data.
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Proteomic study of the therapeutic effect of a DNA vector on cervical cancer cells

Proteomic study of the therapeutic effect of a DNA vector on cervical cancer cells

The purification of mcDNA vectors was performed using size exclusion chromatography sepharose columns (Sephacryl S-1000 SF), showing that for the smallest vector, mcDNA- primiR-375, a 106 mL column allowed the efficient recovery of chromatographic fractions composed only with mcDNA. On the other hand, for the biggest mcDNA vectors, it was necessary to exploit the parameters affecting the sample molecules separation, choosing to use a column with 180 mL of volume, allowing, similarly to the mcDNA-primiR-375 purification, recover fraction only composed with mcDNA. Simultaneously, cytotoxicity assays on human fibroblasts and CaSki cells were performed, confirming that none of the vectors were toxic to the fibroblasts and the mcDNA primiR-375+p53 presented the lower cell viability for CaSki cells. In addition, the proliferation assay results performed on CaSki cells show that number of viable cells decreases for the mcDNA vectors transfected cells, corroborating the cytotoxicity assays results for this cell line. Western-Blot confirmed the re-establishment of tumour suppressor proteins levels after 48h of transfection using mcDNA-p53 and mcDNA- primiR-375+p53.
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Evaluation, prediction and optimization the ultrasound-assisted extraction method using response surface methodology: antioxidant and biological properties of Stachys parviflora L.

Evaluation, prediction and optimization the ultrasound-assisted extraction method using response surface methodology: antioxidant and biological properties of Stachys parviflora L.

Four microorganisms including Escherichia coli (PTCC 1330, Persian Type Culture Collection or ATTC 8739, American Type Culture Collection) and Pseudomonas aeruginosa (PTCC 1074 or ATCC 9027) as Gram-negative bacteria as well as Staphylococcus aureus (PTCC 1337, 1112 or ATCC 29737, 6538 respectively), Staphylococcus epidermidis (PTCC 1114 or ATCC 12228 and ATCC 700576) as Gram-positive bacteria were employed. In vitro antibacterial screening tests were performed using 24 hr growth culture at 37 °C on tryptone soy agar. Briefly, a suspension of each bacterium was prepared in sterile normal saline from its fresh colonies. The turbidity was compared to 0.5 Mcfarland as standard to achieve 10 8 CFU ml -1 . Then the suspension was adjusted to
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