Drosophila: a "model" model system to study neurodegeneration

The fruit fly, Drosophila melanogaster, is a powerful model genetic organism that has been used since the turn of the previous century in the study of complex biological problems. In the last decade, numerous researchers have focused their attention on understanding neurodegenerative diseases by utilizing this model system. Numerous Drosophila mutants have been isolated that profoundly affect neural viability and integrity of the nervous system with age. Additionally, many transgenic strains have been developed as models of human disease conditions. We review the existing Drosophila neurodegenerative mutants and transgenic disease models, and discuss the role of the fruit fly in therapeutic development for neurodegenerative diseases.     

Kinomics: methods for deciphering the kinome

Phosphorylation by protein kinases is the most widespread and well-studied signaling mechanism in eukaryotic cells. Phosphorylation can regulate almost every property of a protein and is involved in all fundamental cellular processes. Cataloging and understanding protein phosphorylation is no easy task: many kinases may be expressed in a cell, and one-third of all intracellular proteins may be phosphorylated, representing as many as 20,000 distinct phosphoprotein states. Defining the kinase complement of the human genome, the kinome, has provided an excellent starting point for understanding the scale of the problem. The kinome consists of 518 kinases, and every active protein kinase phosphorylates a distinct set of substrates in a regulated manner. Deciphering the complex network of phosphorylation-based signaling is necessary for a thorough and therapeutically applicable understanding of the functioning of a cell in physiological and pathological states. We review contemporary techniques for identifying physiological substrates of the protein kinases and studying phosphorylation in living cells.     

Membrane transport: deciphering fusion

Membrane fusion events that occur in yeast have been reconstituted with a minimal set of SNARE protein components. This system has been exploited to establish the syntax underlying specificity of intracellular fusion events from yeast to mammals.     

Calcium signaling: deciphering the calcium-NFAT pathway

Rapid cellular calcium oscillations activate gene expression hours later. How this temporal response amplification is achieved has until now been largely a mystery. An elegant combination of experimental strategies and a model that encompasses non-linear inputs and outputs now sheds new light on this long-standing problem.     

The social network: deciphering fungal language

It has been estimated that up to one quarter of the world's biomass is of fungal origin, comprising approximately 1.5 million species. In order to interact with one another and respond to environmental cues, fungi communicate with their own chemical languages using a sophisticated series of extracellular signals and cellular responses. A new appreciation for the linkage between these chemical languages and developmental processes in fungi has renewed interest in these signalling molecules, which can now be studied using post-genomic resources. In this Review, we focus on the molecules that are secreted by the largest phylum of fungi, the Ascomycota, and the quest to understand their biological function.     

Mammalian sex reversal and intersexuality: deciphering the sex-determination cascade

The sex-determination cascade constitutes a model of the exquisite mechanisms of gene regulation that lead to the development of mammalian embryos. The discovery of the sex-determining region of the Y chromosome (SRY) in the early 1990s was the first crucial step towards a general understanding of sex determination. Since then, several genes that encode proteins with a role in this cascade, such as WT1, SF-1, SOX9, DAX-1 and WNT4, have been identified. Many of the interactions between these proteins have still to be elucidated, while, no-doubt, others are still to be identified. The study of mammalian intersexes forms a promising way towards the identification of the still-missing genes and a comprehensive view of mammalian sex determination. Intersexuality in the goat, studied for over a century, will, presumably, bring to light new genes involved in the female sex-determination pathway.     

Plant aquaporins with non-aqua functions: deciphering the signature sequences

Research in recent years on plant Major Intrinsic Proteins (MIPs), commonly referred to as 'aquaporins', has seen a vast expansion in the substrates found to be transported via these membrane channels. The diversity in sizes, chemical nature and physiological significance of these substrates has meant a need to critically analyse the possible structural and biochemical properties of MIPs that transport these, in order to understand their roles. In this work we have undertaken a comprehensive analysis of all plant MIPs, coming from different families, that have been proven to transport ammonia, boron, carbon dioxide, hydrogen peroxide, silicon and urea. The sequences were analysed for all primary selectivity-related motifs (NPA motifs, ar/R filter, P1-P5 residues). In addition, the putative regulatory phosphorylation and glycosylation sites and mechanistic regulators such as loop lengths have been analysed. Further, nine specificity-determining positions (SDPs) were predicted for each group. The results show the ar/R filter residues, P2-P4 positions and some of the SDPs are characteristic for certain groups, and O-glycosylation sites are unique to a subgroup while N-glycosylation was characteristic of the other MIPs. Certain residues, especially in loop C, and structural parameters such as loop lengths also contribute to the uniqueness of groups. The comprehensive analysis makes significant inroads into appraising the intriguing diversity of plant MIPs and their roles in fundamental life processes, and provides tools for plant selections, protein engineering and transgenics.     

Towards deciphering the Helicobacter pylori cytotoxin

VacA, the major exotoxin produced by Helicobacter pylori, is composed of identical 87 kDa monomers that assemble into flower-shaped oligomers. The monomers can be proteolytically cleaved into two moieties, one of 37 and the other of 58 kDa, named P37 and P58 respectively. The most studied property of VacA is the alteration of intracellular vesicular trafficking in eukaryotic cells leading to the formation of large vacuoles containing markers of late endosomes and lysosomes. However, VacA also causes a reduction in transepithelial electrical resistance in polarized monolayers and forms ion channels in lipid bilayers. The ability to induce vacuoles is localized mostly but not entirely in P37, whereas P58 is mostly involved in cell targeting. Until recently, H. pylori isolates were classified as tox+ or tox-, depending on whether they induced vacuoles in HeLa cells or not. Today, we know that almost all strains are cytotoxic. The major difference between tox+ and tox- resides in the cell binding domain, which exists in two allelic forms, only one of which is toxic for HeLa cells. The two forms, named m1 and m2, are found predominantly in Western and Chinese isolates respectively.