Novel method for analysis of allele specific expression in triploid Oryzias latipes reveals consistent pattern of allele exclusion.

Assessing allele-specific gene expression (ASE) on a large scale continues to be a technically challenging problem. Certain biological phenomena, such as X chromosome inactivation and parental imprinting, affect ASE most drastically by completely shutting down the expression of a whole set of alleles. Other more subtle effects on ASE are likely to be much more complex and dependent on the genetic environment and are perhaps more important to understand since they may be responsible for a significant amount of biological diversity.

Transcriptomic analysis of cultured whale skin cells exposed to hexavalent chromium [Cr(VI)].

Hexavalent chromium Cr(VI) is known to produce cytotoxic effects in humans and is a highly toxic environmental contaminant. Interestingly, it has been shown that free ranging sperm whales (Phyester macrocephalus) may have exceedingly high levels of Cr in their skin. Also, it has been demonstrated that skin cells from whales appear more resistant to both cytotoxicity and clastogenicity upon Cr exposure compared to human cells.

Alternative strategies for development of a reference transcriptome for quantification of allele specific expression in organisms having sparse genomic resources.

In recent years RNA-Seq technology has been used not only to quantify differences in gene expression but also to understand the underlying mechanisms that lead to these differences. Nucleotide sequence variation arising through evolution may differentially affect the expression profiles of divergent species. RNA-Seq technology, combined with techniques to differentiate parental alleles and quantify their abundance, have recently become popular methods for allele specific gene expression (ASGE) analyses.

Comparison analysis of primary ligand-binding sites in seven-helix membrane proteins.

Seven-helix transmembrane proteins, including the G-protein-coupled receptors (GPCRs), mediate a broad range of fundamental cellular activities through binding to a wide range of ligands. Understanding the structural basis for the ligand-binding selectivity of these proteins is of significance to their structure-based drug design. Comparison analysis of proteins' ligand-binding sites provides a useful way to study their structure-activity relationships.

Comparative analysis of the packing topology of structurally important residues in helical membrane and soluble proteins.

Elucidating the distinct topology of residue packing in transmembrane proteins is essential for developing high-quality computational tools for their structure prediction. Network approaches transforming a protein's three-dimensional structure into a network have proven useful in analyzing various aspects of protein structures. Residues with high degree of connectivity as identified through network analysis are considered to be important for the stability of a protein's folded structure.

Network pattern of residue packing in helical membrane proteins and its application in membrane protein structure prediction.

De novo protein structure prediction plays an important role in studies of helical membrane proteins as well as structure-based drug design efforts. Developing an accurate scoring function for protein structure discrimination and validation remains a current challenge. Network approaches based on overall network patterns of residue packing have proven useful in soluble protein structure discrimination.