A Gene-Specific Method for Predicting Hemophilia-Causing Point Mutations

A fundamental goal of medical genetics is the accurate prediction of genotype–phenotype correlations. As an approach to develop more accurate in silico tools for prediction of disease-causing mutations of structural proteins, we present a gene- and disease-specific prediction tool based on a large systematic analysis of missense mutations from hemophilia A (HA) patients. Our HA-specific prediction tool, HApredictor, showed disease prediction accuracy comparable to other publicly available prediction software. In contrast to those methods, its performance is not limited to non-synonymous mutations. Given the role of synonymous mutations in disease and drug codon optimization, we propose that utilizing a gene- and disease-specific method can be highly useful to make functional predictions possible even for synonymous mutations. Incorporating computational metrics at both nucleotide and amino acid levels along with multiple protein sequence/structure alignment significantly improved the predictive performance of our tool. HApredictor is freely available for download at http://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/HA_Predict/index.htm.     

Small molecules restore the function of mutant CLC5 associated with Dent disease

Dent disease type 1 is caused by mutations in the CLCN5 gene that encodes CLC5, a 2Cl⁻/H⁺ exchanger. The CLC5 mutants that have been functionally analysed constitute three major classes based on protein expression, cellular localization and channel function. We tested two small molecules, 4-phenylbutyrate (4PBA) and its analogue 2-naphthoxyacetic acid (2-NOAA), for their effect on mutant CLC5 function and expression by whole-cell patch-clamp and Western blot, respectively. The expression and function of non-Class I CLC5 mutants that have reduced function could be restored by either treatment. Cell viability was reduced in cells treated with 2-NOAA. 4PBA is a FDA-approved drug for the treatment of urea cycle disorders and offers a potential therapy for Dent disease.     

Abnormal stomatal behavior and root resistance,and hormonal imbalance in three wilty mutants of tomato

Three wilty mutants of tomato, flacca, sitiens, and notabilis, were compared with two control normal cultivars, Rheinlands Ruhm and Lukullus, for concentration of abscisic acid and root resistance to water flow. In addition, the three mutants treated with abscisic acid during development were compared with control mutant plants for stomatal opening and root resistance. The hormonal concentration was estimated by coleoptile assay and gas chromatography. Stomatal opening was estimated by measuring rate of transpiration and by examining leaf imprints. Root resistance was estimated by measuring the amount of exudate from roots of decapitated plants and the difference between the osmotic pressure of the exudate and the root medium. A lower level of abscisic acid was found in all three mutants as compared with the control normal plants. In addition, root resistance to water flow was higher in the three mutants than in the control normal types. All three mutants completely reverted to normal phenotypically, including stomatal and root resistances, when treated with abscisic acid. It has been suggested that the first hormonal change in the mutants is that of abscisic acid, and from it proceed the other changes.This work was supported in part by a research grant from the Ford Foundation (Ford-6, A-VII).     

Alveolar dehiscences and fenestrae in dried south African Negro mandibles

The buccal and lingual roots of 1077 teeth from 100 mandibles of South African Negroes were examined for the presence of dehiscences and fenestrae. All specimens were obtained from cadavers of known sex, tribe, and stated age; 10.5% of teeth were affected. Canines and first premolars were the most common teeth associated with dehiscences and fenestrae. Dehiscences occurred more commonly than fenestrae (1:0.49). The defects were found exclusively in the buccal plate of the alveolar process.     

The metabolism of abscisic acid in flacca,a wilty mutant of tomato

The wilty tomato mutant flacca and the normal variety Rheinlands Ruhm were used in this research. The mutant phenotype was explained mainly by hormonal changes. One of these, the decrease in abscisic acid level, was suggested as the hormonal change closest to the mutated gene. The cause of the lower abscisic acid level in the mutant, which may be enhanced breakdown or inactivation, or inhibited biosynthesis, was investigated. The first possibility was studied by comparing mutant and normal plants treated with t-abscisic acid-2-C¹⁴ for (1) rate of production of labeled methanol-extractable metabolites and (2) radioactivity remaining in the methanol-unextractable fraction. The level of trans, trans-abscisic acid relative to that of cis,trans-abscisic acid was studied in untreated plants. Only two radioactive regions containing metabolites of abscisic acid were detected from either of the plant types, and their rates of production relative to total radioactivity was equal. The radioactivity in the methanolunextractable fraction and the level of trans,trans-abscisic acid were very low in both mutant and normal plants. The second possibility was studied partly by comparing the levels of various xanthophylls in mutant and normal plants and their effect after illumination on cress seed germination. Xanthophylls of both plant types were identical in their absorption spectra, but their levels were higher in the mutant. Of these xanthophylls, illuminated neoxanthin inhibited seed germination in both plant types, but more effectively in the mutant. The most probable explanation for the low level of cis,trans-abscisic acid in flacca is that the conversion of farnesyl PiP to abscisic acid is inhibited in this plant.     

Colonization dynamics of Pantoea agglomerans in the wheat root habitat

Plants are colonized by microbial communities that have diverse implications for plant development and health. The establishment of a stable plant–bacteria interaction depends on a continuous coexistence over generations. Transmission via the seed is considered as the main route for vertical inheritance of plant-associated bacteria. Nonetheless, the ecological principles that govern the plant colonization by seed endophytes remain understudied. Here we quantify the contribution of arrival time and colonization history to bacterial colonization of the wheat root. Establishing a common seed endophyte, Pantoea agglomerans, and wheat as a model system enabled us to document bacterial colonization of the plant roots during the early stages of germination. Using our system, we estimate the carrying capacity of the wheat roots as 10⁸ cells g⁻¹, which is robust among individual plants and over time. Competitions in planta reveal a significant advantage of early incoming colonizers over late-incoming colonizers. Priming for the wheat environment had little effect on the colonizer success. Our experiments thus provide empirical data on the root colonization dynamics of a seed endophyte. The persistence of seed endophyte bacteria with the plant population over generations may contribute to the stable transmission that is one route for the evolution of a stable host-associated lifestyle.     

Work that body: fin and body movements determine herbivore feeding performance within the natural reef environment

Herbivorous fishes form a keystone component of reef ecosystems, yet the functional mechanisms underlying their feeding performance are poorly understood. In water, gravity is counter-balanced by buoyancy, hence fish are recoiled backwards after every bite they take from the substrate. To overcome this recoil and maintain contact with the algae covered substrate, fish need to generate thrust while feeding. However, the locomotory performance of reef herbivores in the context of feeding has hitherto been ignored. We used a three-dimensional high-speed video system to track mouth and body kinematics during in situ feeding strikes of fishes in the genus Zebrasoma, while synchronously recording the forces exerted on the substrate. These herbivores committed stereotypic and coordinated body and fin movements when feeding off the substrate and these movements determined algal biomass removed. Specifically, the speed of rapidly backing away from the substrate was associated with the magnitude of the pull force and the biomass of algae removed from the substrate per feeding bout. Our new framework for measuring biting performance in situ demonstrates that coordinated movements of the body and fins play a crucial role in herbivore foraging performance and may explain major axes of body and fin shape diversification across reef herbivore guilds.