From biological databases to platforms for biomedical discovery

The use of high-throughput DNA sequencing and proteomic methods has led to an unprecedented increase in the amount of genomic and proteomic data. Application of computing technologies and development of computational tools to analyze and present these data has not kept pace with the accumulation of information. Here, we discuss the use of different database systems to store biological information and mention some of the key emerging computing technologies that are likely to have a key role in the future of bioinformatics.     

The NFP locus of Medicago truncatula controls an early step of Nod factor signal transduction upstream of a rapid calcium flux and root hair deformation

Establishment of the Rhizobium-legume symbiosis depends on a molecular dialogue, in which rhizobial nodulation (Nod) factors act as symbiotic signals, playing a key role in the control of specificity of infection and nodule formation. Using nodulation-defective (Nod-) mutants of Medicago truncatula to study the mechanisms controlling Nod factor perception and signalling, we have previously identified five genes that control components of a Nod factor-activated signal transduction pathway. Characterisation of a new M. truncatula Nod- mutant led to the identification of the Nod Factor Perception (NFP) locus. The nfp mutant has a novel phenotype among Nod- mutants of M. truncatula, as it does not respond to Nod factors by any of the responses tested. The nfp mutant thus shows no rapid calcium flux, the earliest detectable Nod factor response of wild-type plants, and no root hair deformation. The nfp mutant is also deficient in Nod factor-induced calcium spiking and early nodulin gene expression. While certain genes controlling Nod factor signal transduction also control the establishment of an arbuscular mycorrhizal symbiosis, the nfp mutant shows a wild-type mycorrhizal phenotype. These data indicate that the NFP locus controls an early step of Nod factor signal transduction, upstream of previously identified genes and specific to nodulation.     

Pervaporative stripping of acetone, butanol and ethanol to improve ABE fermentation

Acetone-butanol-ethanol fermentation by anaerobic bacterium C. acetobutylicum is a potential source for feedstock chemicals. The problem of product induced inhibition makes this fermentation economically infeasible. Pervaporation is studied as an effective separation technique to remove the toxic inhibitory products. Various membranes like Styrene Butadiene Rubber (SBR), Ethylene Propylene Diene Rubber (EPDM), plain Poly Dimethyl Siloxane (PDMS) and silicalite filled PDMS were studied for the removal of acetone, butanol and ethanol, from binary aqueous mixtures and from a quaternary mixture. It was found that the overall performance of PDMS filled with 15% w/w of silicalite was the best for removal of butanol in binary mixture study. SBR performance was best for the quaternary mixture studied.     

Fructose-mediated damage to lens alpha-crystallin: prevention by pyruvate

Post-translational modifications in lens crystallins due to glycation and oxidation have been suggested to play a significant role in the development of cataracts associated with aging and diabetes. We have previously shown that alpha-keto acids, like pyruvate, can protect the lens against oxidation. We hypothesize that they can also prevent the glycation of proteins competitively by forming a Schiff base between their free keto groups and the free -NH(2) groups of protein as well as subsequently inhibit the oxidative conversion of the initial glycation product to advanced glycation end products (AGE). The purpose of this study was to investigate these possibilities using purified crystallins. The crystallins isolated from bovine lenses were incubated with fructose in the absence and presence of pyruvate. The post-incubation mixtures were analyzed for fructose binding to the crystallins, AGE formation, and the generation of high molecular weight (HMW) proteins. In parallel experiments, the keto acid was replaced by catalase, superoxide dismutase (SOD), or diethylene triaminepentaacetic acid (DTPA). This was done to ascertain oxidative mode of pyruvate effects. Interestingly, the glycation and consequent formation of AGE from alpha-crystallin was more pronounced than from beta-, and gamma-crystallins. The changes in the crystallins brought about by incubation with fructose were prevented by pyruvate. Catalase, SOD, and DTPA were also effective. The results suggest that pyruvate prevents against fructose-mediated changes by inhibiting the initial glycation reaction as well as the conversion of the initial glycated product to AGE. Hence it is effective in early as well as late phases of the reactions associated with the formation of HMW crystallin aggregates.     

Putative Location of Common Region and Coat Protein Gene of Blackgram Isolate of Mungbean Yellow Mosaic Geminivirus

Reciprocal cross hybridization between DNA-A and ONA-B molecules showed that MYMV genome contains certain regions common to each other. “Common region” of MYMV belongs to the 0.55 kb Kpnl-Clal fragment of DNA-A and 0.25 kb Xbal-Hind III fragment of DNA-B. Hybridization of DNA-A restriction fragments with the full length coat protein region probe to Indian cassava mosaic virus (ICMV) showed the location of MYMV coat protein coding region in DNA-A. The greater extent of homology of ICMV coat protein region falls within the 400 base pair region of Clal-Clal fragment in DNA-A of MYMV-Bg. The homology between ICMV and MYMV-Bg coat protein gene appeared to be less than 50%. Cross hybridization between DNA-A and DNA-B molecules helped to trim out the homologous region and the DNA-A and DNA-B specific probes could be tailored.     

Airway mechanics, gas exchange, and blood flow in a nonlinear model of the normal human lung

Amodel integrating airway/lung mechanics, pulmonary blood flow, and gasexchange for a normal human subject executing the forced vital capacity(FVC) maneuver is presented. It requires as input the intrapleuralpressure measured during the maneuver. Selected model-generated outputvariables are compared against measured data (flow at the mouth, changein lung volume, and expired O₂ and CO₂concentrations at the mouth). A nonlinear parameter-estimation algorithm is employed to vary selected sensitive model parameters toobtain reasonable least squares fits to the data. This study indicatesthat 1) all three components of the respiratory model arenecessary to characterize the FVC maneuver; 2) changes in pulmonary blood flow rate are associated with changes in alveolar andintrapleural pressures and affect gas exchange and the time course ofexpired gas concentrations; and 3) a collapsible midairway segment must be included to match airflow during a forced expiration. Model simulations suggest that the resistances to airflow offered bythe collapsible segment and the small airways are significant throughout forced expiration; their combined effect is needed toadequately match the inspiratory and expiratory flow-volume loops.Despite the limitations of this lumped single-compartment model, aremarkable agreement with airflow and expired gas concentration measurements is obtained for normal subjects. Furthermore, the modelprovides insight into the important dynamic interactions betweenventilation and perfusion during the FVC maneuver.

     

Disintegration Mediated Controlled Release Supersaturating Solid Dispersion Formulation of an Insoluble Drug: Design,Development, Optimization,and In Vitro Evaluation

The objective of this study was to develop a solid dispersion based controlled release system for drug substances that are poorly soluble in water. A wax-based disintegration mediated controlled release system was designed based on the fact that an amorphous drug can crystallize out from hydrophilic matrices. For this study, cilostazol (CIL) was selected as the model drug, as it exhibits poor aqueous solubility. An amorphous solid dispersion was prepared to assist the drug to attain a supersaturated state. Povidone was used as carrier for solid dispersion (spray drying technique), hydrogenated vegetable oil (HVO) as wax matrix former, and sodium carboxymethyl cellulose (NaCMC) as a disintegrant. The extreme vertices mixture design (EVMD) was applied to optimize the designed and developed composition. The optimized formulation provided a dissolution pattern which was equivalent to the predicted curve, ascertaining that the optimal formulation could be accomplished with EVMD. The release profile of CIL was described by the Higuchi’s model better than zero-order, first-order, and Hixson-Crowell’s model, which indicated that the supersaturation state of CIL dominated to allow drug release by diffusion rather than disintegration regulated release as is generally observed by Hixson-Crowell’s model. The optimized composition was evaluated for disintegration, dissolution, XRD, and stability studies. It was found that the amorphous state as well as the dissolution profile of CIL was maintained under the accelerated conditions of 40°C/75% RH for 6 months.KEY WORDS: cilostazol, controlled release, disintegration-mediated controlled release (DMCR), extreme vertices mixture design (EVMD), solid dispersion     

Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny,Physiology, and Niche Adaptation on Human Skin

Malassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina, (Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens. Malassezia are typically isolated from warm-blooded animals, are dominant members of the human skin mycobiome and are associated with common skin disorders. To characterize the genetic basis of the unique phenotypes of Malassezia spp., we sequenced the genomes of all 14 accepted species and used comparative genomics against a broad panel of fungal genomes to comprehensively identify distinct features that define the Malassezia gene repertoire: gene gain and loss; selection signatures; and lineage-specific gene family expansions. Our analysis revealed key gene gain events (64) with a single gene conserved across all Malassezia but absent in all other sequenced Basidiomycota. These likely horizontally transferred genes provide intriguing gain-of-function events and prime candidates to explain the emergence of Malassezia. A larger set of genes (741) were lost, with enrichment for glycosyl hydrolases and carbohydrate metabolism, concordant with adaptation to skin’s carbohydrate-deficient environment. Gene family analysis revealed extensive turnover and underlined the importance of secretory lipases, phospholipases, aspartyl proteases, and other peptidases. Combining genomic analysis with a re-evaluation of culture characteristics, we establish the likely lipid-dependence of all Malassezia. Our phylogenetic analysis sheds new light on the relationship between Malassezia and other members of Ustilaginomycotina, as well as phylogenetic lineages within the genus. Overall, our study provides a unique genomic resource for understanding Malassezia niche-specificity and potential virulence, as well as their abundance and distribution in the environment and on human skin.