Thermotropic gelation of ovalbumin: 2. Boundary conditions on the formation and the concentration dependence of equilibrium elastic modulus for thermotropic ovalbumin gels

Studies were made on the boundary conditions for thermotropic ovalbumin gelation at pH within the range 2.5 to 10.0. The pH dependence of the gelation threshold, C₀, and denaturation temperature, T_d, were obtained. The dependence C₀(pH) has a sharp minimum close to the isoelectric point (pl). Over pH range 2.5 to 4.0 the dependence T_d(pH) is linear; although above pI it shows unusual behaviour. T_d increases smoothly, becoming a constant value (T_d=80°C) at pH 7. Analysis of the temperature dependence of Leu's line integral intensity in the p.m.r. spectrum of ovalbumin shows that the temperature threshold of thermotropic gelation closely approximates to T_d. A diagram for the state of an ovalbumin -water system was constructed in temperature-concentration-pH coordinates. The dependences of the initial shear modulus for thermotropic ovalbumin gels on the concentration (0.06≤C≤0.25g/cm³ were obtained at pH 4.0, 7.0, 8.5, 10.0. They are equivalent to the concentration dependence of the equilibrium elastic modulus E_e(C). The dependences obtained may be reduced to the theoretical master dependence of Hermans, $\text{E}{}_{\mathrm{e}}\text{(rm}\text{C}\text{?}\text{)}$, where $\text{C}\text{?}\text{=}\text{C}\text{/}\text{C}{}_0$ is the reduced concentration. Hermans' theory, based o the model for random cross-linking of linear identical macromolecules without cyclization, adequately describes the equilibrium elastic properties of thermotropic ovalbumin gels.     

Statistical geometry based prediction of nonsynonymous SNP functional effects using random forest and neuro-fuzzy classifiers

There is substantial interest in methods designed to predict the effect of nonsynonymous single nucleotide polymorphisms (nsSNPs) on protein function, given their potential relationship to heritable diseases. Current state-of-the-art supervised machine learning algorithms, such as random forest (RF), train models that classify single amino acid mutations in proteins as either neutral or deleterious to function. However, it is frequently the case that the functional effect of a polymorphism on a protein resides between these two extremes. The utilization of classifiers that incorporate fuzzy logic provides a natural extension in order to account for the spectrum of possible functional consequences. We generated a dataset of single amino acid substitutions in human proteins having known three-dimensional structures. Each variant was uniquely represented as a feature vector that included computational geometry and knowledge-based statistical potential predictors obtained though application of Delaunay tessellation of protein structures. Additional attributes consisted of physicochemical properties of the native and replacement amino acids as well as topological location of the mutated residue position in the solved structure. Classification performance of the RF algorithm was evaluated on a training set consisting of the disease-associated and neutral nsSNPs taken from our dataset, and attributes were ranked according to their relative importance. Similarly, we evaluated the performance of adaptive neuro-fuzzy inference system (ANFIS). The utility of statistical geometry predictors was compared with that of traditional structural and evolutionary attributes employed by other researchers, revealing an equally effective yet complementary methodology. Among all attributes in our feature set, the statistical geometry predictors were found to be the most highly ranked. On the basis of the AUC (area under the ROC curve) measure of performance, the ANFIS and RF models were equally effective when only statistical geometry features were utilized. Tenfold cross-validation studies evaluating AUC, balanced error rate (BER), and Matthew's correlation coefficient (MCC) showed that our RF model was at least comparable with the well-established methods of SIFT and PolyPhen. The trained RF and ANFIS models were each subsequently used to predict the disease potential of human nsSNPs in our dataset that are currently unclassified (http://rna.gmu.edu/FuzzySnps/).     

Cell surface expression of CD147/EMMPRIN is regulated by cyclophilin 60

CD147, also known as extracellular matrix metalloproteinase inducer, is a regulator of matrix metalloproteinase production and also serves as a signaling receptor for extracellular cyclophilins. Previously, we demonstrated that cell surface expression of CD147 is sensitive to cyclophilin-binding drug cyclosporin A, suggesting involvement of a cyclophilin in the regulation of intracellular transport of CD147. In this report, we identify this cyclophilin as cyclophilin 60 (Cyp60), a distinct member of the cyclophilin family of proteins. CD147 co-immunoprecipitated with Cyp60, and confocal immunofluorescent microscopy revealed intracellular co-localization of Cyp60 and CD147. This interaction with Cyp60 involved proline 211 of CD147, which was shown previously to be critical for interaction between CD147 and another cyclophilin, cyclophilin A, in solution. Mutation of this proline residue abrogated co-immunoprecipitation of CD147 and Cyp60 and reduced surface expression of CD147 on the plasma membrane. Suppression of Cyp60 expression using RNA interference had an effect similar to that of cyclosporin A: reduction of cell surface expression of CD147. These results suggest that Cyp60 plays an important role in the translocation of CD147 to the cell surface. Therefore, Cyp60 may present a novel target for therapeutic interventions in diseases where CD147 functions as a pathogenic factor, such as cancer, human immunodeficiency virus infection, or rheumatoid arthritis.     

Distal trisomy 10q and limb defects

Analysis of the literature showed that hypoplasia (or aplasia) of tibiae was found at least in six persons with trisomy 10q25.2-qter. Therefore, these defects should be considered as a characteristic manifestation of the distal trisomy 10q. In most of these patients, tibial abnormalities were associated with other defects of the lower extremities (hypoplastic femora, ectrodactyly, preaxial polydactyly). Upper limbs were affected in one patient (as well as in her sib without tibial defects). Most likely, segment 10q25.2-qter contains a gene which (when triplicated) leads to maldevelopment of the limbs, and tibial malformations are only one manifestation of this field defect.     

Cellular redox-status is associated with regulation of frond division in <Emphasis Type="Italic">Spirodela polyrrhiza</Emphasis>

We investigated a possible relationship between the levels of reactive oxygen species (ROS) and the stimulation of frond division of the aquatic plant Spirodela polyrrhiza (duckweed) during a 7-day experimental culture period. In particular, we monitored superoxide concentration using a state-of-the-art cell biosensor. A considerable reduction in ROS and superoxide concentration was observed during the first 2 days of culture, whereas duckweed cultures achieved near exponential growth rates after the second day. In addition, apoptotic markers such as the cytoplasmic concentration of cytochrome c, mitochondrial membrane depolarization and the activity of caspase-3 declined during the culture period and at least before daughter frond maturation. We suggest that S. polyrrhiza frond division may have been stimulated by the observed reduction of free radicals and the associated avoidance of cell apoptotic pathways in cultured plants.     

Knowledge-based computational mutagenesis for predicting the disease potential of human non-synonymous single nucleotide polymorphisms

Certain genetic variations in the human population are associated with heritable diseases, and single nucleotide polymorphisms (SNPs) represent the most common form of such differences in DNA sequence. In particular, substantial interest exists in determining whether a non-synonymous SNP (nsSNP), leading to a single residue replacement in the translated protein product, is neutral or disease-related. The nature of protein structure-function relationships suggests that nsSNP effects, either benign or leading to aberrant protein function possibly associated with disease, are dependent on relative structural changes introduced upon mutation. In this study, we characterize a representative sampling of 1790 documented neutral and disease-related human nsSNPs mapped to 243 diverse human protein structures, by quantifying environmental perturbations in the associated proteins with the use of a computational mutagenesis methodology that relies on a four-body, knowledge-based, statistical contact potential. These structural change data are used as attributes to generate a vector representation for each nsSNP, in combination with additional features reflecting sequence and structure of the corresponding protein. A trained model based on the random forest supervised classification algorithm achieves 76% cross-validation accuracy. Our classifier performs at least as well as other methods that use significantly larger datasets of nsSNPs for model training, and the novelty of our attributes differentiates the model as an orthogonal approach that can be utilized in conjunction with other techniques. A dedicated server for obtaining predictions, as well as supporting datasets and documentation, is available at http://proteins.gmu.edu/automute.     

The pyruvate-lactate axis modulates cardiac hypertrophy and heart failure

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High ethanol yields using Aspergillus oryzae koji and corn media

Summary High ethanol and stillage solids have been achieved using whole corn mashes. Ethanol yields of 14% (v/v) (89.5% of theory) and stillage levels of approximately 23% (w/v) were obtained in 74–90 hours using mild acid pretreatment with Aspergillus oryzae wheat bran koji saccharification. High ethanol yields were also obtained with bacterial amylase, instead of the acid treatment, when the sterilization step was omitted. The implications of ethanol fermentation process modifications are explored.