Morels: the story so far

True morels, among the most glamorous and highly valued edible fungi, have been in the midst of taxonomical controversies for over a century. The use of molecular phylogenetic techniques and integrative taxonomical approaches have in recent years revolutionised our understanding of morels, resolving many of the old debates, but also giving rise to new ones. This review summarises the advances made and challenges met, with regards to this fascinating genus.     

Transducing Hedgehog: the story so far.

The secreted proteins of the Hedgehog family have been implicated in many different processes in vertebrate development including cartilage differentiation, myotome and sclerotome specification, hair follicle development, limb morphogenesis and the specification of different neuronal cell types. In addition, the aberrant activation of the Hedgehog pathway has been identified as the likely cause of a number of tumours in humans including basal cell carcinomas (BCCs) and primitive neurectodermal tumours (PNETs). Elucidating the mechanisms by which Hedgehog signals are transduced will thus have widespread implications for our understanding of both normal development and disease.     

Pollen stigma interactions: so near yet so far

Getting a firm grip on the 'S' (incompatibility)-loci, which encourage outbreeding in many flowering plants, continues to be a frustrating exercise. Only last year it seemed that all the male and female S-locus factors that regulate self-incompatibility in a key group of plants - Brassica - had at last been characterized. However, it now appears that the first S-locus product to be identified, does not, after all, play a part in determining S-specificity.     

Carotenoids and bacterial photosynthesis: The story so far...

This concise review describes the current status of research into how carotenoids function in bacterial photosynthesis. This is illustrated by reference to very recent studies on both the photoprotective and antenna functions of carotenoids. The major remaining open questions on the detailed molecular mechanisms involved in these reactions are highlighted. This revised version was published online in June 2006 with corrections to the Cover Date.     

Molecular abnormalities in leukemia: the 11q23 story so far

Various hematopoietic malignant disorders have been shown to bear chromosome abnormalities of the 11q23 band, which can be rearranged with many different chromosomal regions in a wide variety of different leukemia subtypes. Several laboratories have identified a trithorax-related gene that is involved in most of the 11q23 abnormalities. Although some patterns and associations between the partner genes are beginning to emerge, it is not yet possible to frame a single unifying hypothesis for 11q23 leukaemic transformation. The aim of this review is to summarise the recent data concerning these 11q23 rearrangements and the understanding of their consequences.     

DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions

The structures of DNA-protein complexes have illuminated the diversity of DNA-protein binding mechanisms shown by different protein families. This lack of generality could pose a great challenge for predicting DNA-protein interactions. To address this issue, we have developed a knowledge-based method, DNA-binding Domain Hunter (DBD-Hunter), for identifying DNA-binding proteins and associated binding sites. The method combines structural comparison and the evaluation of a statistical potential, which we derive to describe interactions between DNA base pairs and protein residues. We demonstrate that DBD-Hunter is an accurate method for predicting DNA-binding function of proteins, and that DNA-binding protein residues can be reliably inferred from the corresponding templates if identified. In benchmark tests on approximately 4000 proteins, our method achieved an accuracy of 98% and a precision of 84%, which significantly outperforms three previous methods. We further validate the method on DNA-binding protein structures determined in DNA-free (apo) state. We show that the accuracy of our method is only slightly affected on apo-structures compared to the performance on holo-structures cocrystallized with DNA. Finally, we apply the method to approximately 1700 structural genomics targets and predict that 37 targets with previously unknown function are likely to be DNA-binding proteins. DBD-Hunter is freely available at http://cssb.biology.gatech.edu/skolnick/webservice/DBD-Hunter/.     

Protein-DNA interactions: A structural analysis

A detailed analysis of the DNA-binding sites of 26 proteins is presented using data from the Nucleic Acid Database (NDB) and the Protein Data Bank (PDB). Chemical and physical properties of the protein-DNA interface, such as polarity, size, shape, and packing, were analysed. The DNA-binding sites shared common features, comprising many discontinuous sequence segments forming hydrophilic surfaces capable of direct and water-mediated hydrogen bonds. These interface sites were compared to those of protein-protein binding sites, revealing them to be more polar, with many more intermolecular hydrogen bonds and buried water molecules than the protein-protein interface sites. By looking at the number and positioning of protein residue-DNA base interactions in a series of interaction footprints, three modes of DNA binding were identified (single-headed, double-headed and enveloping). Six of the eight enzymes in the data set bound in the enveloping mode, with the protein presenting a large interface area effectively wrapped around the DNA.A comparison of structural parameters of the DNA revealed that some values for the bound DNA (including twist, slide and roll) were intermediate of those observed for the unbound B-DNA and A-DNA. The distortion of bound DNA was evaluated by calculating a root-mean-square deviation on fitting to a canonical B-DNA structure. Major distortions were commonly caused by specific kinks in the DNA sequence, some resulting in the overall bending of the helix. The helix bending affected the dimensions of the grooves in the DNA, allowing the binding of protein elements that would otherwise be unable to make contact. From this structural analysis a preliminary set of rules that govern the bending of the DNA in protein-DNA complexes, are proposed.     

Ligand-receptor interactions: a new method for determining the binding parameters

A new experimental procedure and new plot coordinates that allow determination of the binding parameters of ligand-acceptor interaction have been proposed. Instead of titration of a constant concentration of receptors with changing concentrations of ligand, as requested by the well-known methods of Klotz and Scatchard, a series of sequential dilutions of the reacting ligand-receptor mixture is suggested. This allows the application of a new coordinate system that transforms the binding isotherms into straight lines. The case of one acceptor with two classes of receptors with different binding constants is also considered briefly, where the correspondent graphs are nonlinear. It is suggested that in some cases this approach can be a simple and convenient substitute of the broadly used methods of Klotz and Scatchard.     

GeneSplicer: a new computational method for splice site prediction

GeneSplicer is a new, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been tested successfully using DNA from two reference organisms: the model plant Arabidopsis thaliana and human. It was compared to six programs representing the leading splice site detectors for each of these species: NetPlantGene, NetGene2, HSPL, NNSplice, GENIO and SpliceView. In each case GeneSplicer performed comparably to the best alternative, in terms of both accuracy and computational efficiency.     

Molluscan genomics: the road so far and the way forward

Hydrobiologia - Mollusca is the second most species-rich phylum within the metazoans, displaying critical economic, ecological and scientific importance. Yet, they are still largely...     

Protein-DNA interactions at recognition sites for the dioxin-Ah receptor complex

Gel retardation analyses reveal a cluster of six binding sites for the liganded Ah receptor within a 700-base pair DNA domain upstream of the mouse CYP1A1 gene. The nucleotide sequences of the binding sites define a consensus recognition motif for the liganded receptor. The consensus motif is not symmetric. Alteration of the consensus motif produces a decrease in the receptor-DNA interaction. The ligand receptor binds as a monomer to its recognition motif and preferentially binds to double-stranded DNA. These observations reveal apparent differences between 2,3,7,8-tetrachlorodibenzo-p-dioxin and steroid hormones in their respective mechanisms of action.     

Invasive species in Southeast Asia: the knowledge so far

This review deals with alien species invasion in Southeast Asia, an important conservation and management concern in the region. I report on the current and potential future impacts of biological invasions on biodiversity in Southeast Asia. Current knowledge of the invasive species in Southeast Asia is mostly based on anecdotal observations. Nevertheless, I attempt to compile existing empirical evidence on the negative effects of the biological invaders found in the region. These impacts include displacement of native biota, modification of ecosystems, hybridization, environmental disturbance, and economic loss. Any effective counter-measure will need to involve a multi-national strategy, yet such measure is challenging due to a broad spectrum of political and economic development models among the Southeast Asian countries. An overview of the taxonomic structure of the invasive species in Southeast Asia shows that the invasive plant and fish are the most represented taxonomic groups in all countries. The current research effort in invasion ecology from Southeast Asia is not being up to international standard in comparison to other regions, and the absence of recent international journal articles on invasive plant species reveals the biases in biological invasion-related research. The lack of research capacity and financial support from governments, and the inability to disseminate scholarly data in international journals are the possible reasons for the dearth of research literature on biological invasions from the region. Finally, a forward-looking agenda for the region should include improving the quality and quantity of biological invasion research; adopting a tough approach to the illegal release of wildlife; and applying multi-national strategies that integrate data sharing, prioritization, public awareness, policy work, capacity building, conservation actions and surveillance.