Missing value imputation for epistatic MAPs

Background  

Epistatic miniarray profiling (E-MAPs) is a high-throughput approach capable of quantifying aggravating or alleviating genetic interactions between gene pairs. The datasets resulting from E-MAP experiments typically take the form of a symmetric pairwise matrix of interaction scores. These datasets have a significant number of missing values - up to 35% - that can reduce the effectiveness of some data analysis techniques and prevent the use of others. An effective method for imputing interactions would therefore increase the types of possible analysis, as well as increase the potential to identify novel functional interactions between gene pairs. Several methods have been developed to handle missing values in microarray data, but it is unclear how applicable these methods are to E-MAP data because of their pairwise nature and the significantly larger number of missing values. Here we evaluate four alternative imputation strategies, three local (Nearest neighbor-based) and one global (PCA-based), that have been modified to work with symmetric pairwise data.     

Cytoskeletal connections: building strong cells in new ways

Cell and tissue integrity requires the coordination of actin and microtubules and the linkage of these cytoskeletal elements to cell junctions. New findings reveal that the cytoskeletal linker protein Short stop works with EB1 and APC1 to help carry out this function.     

Laccase: new functions for an old enzyme

Laccases occur widely in fungi; they have been characterized less frequently in higher plants. Here we have focused on more recent reports on the occurrence of laccase and its functions in physiological development and industrial utility. The reports of molecular weights, pH optima, and substrate specificity are extremely diverse. Conclusive proof of the occurrence of laccase in a tissue must demonstrate that the enzyme be able to oxidize quinol with concomitant uptake of oxygen. Laccase is involved in the pigmentation process of fungal spores, the regeneration of tobacco protoplasts, as fungal virulence factors, and in lignification of cell walls and delignification during white rot of wood. Commercially, laccases have been used to delignify woody tissues, produce ethanol, and to distinguish between morphine and codeine. A very wide variety of bioremediation processes employ laccase in order to protect the environment from damage caused by industrial effluents. Research in recent years has been intense, much of it elicited by the wide diversity of laccases, their utility and their very interesting enzymology.     

Freezer anthropology: new uses for old blood

Archived blood fractions (plasma, settled red cells, white cells) have proved to be a rich and valuable source of DNA for human genetic studies. Large numbers of such samples were collected between 1960 and the present for protein and blood group studies, many of which are languishing in freezers or have already been discarded. More are discarded each year because the usefulness of these samples is not widely understood. Data from DNA derived from 10-35-year-old blood samples have been used to address the peopling of the New World and of the Pacific. Mitochondrial DNA haplotypes from studies using this source DNA support a single wave of migration into the New World (or a single source population for the New World), and that Mongolia was the likely source of the founding population. Data from Melanesia have shown that Polynesians are recent immigrants into the Pacific and did not arise from Melanesia.     

CaMKII: new tricks for an old dog

Calcium/calmodulin-dependent protein kinase II (CaMKII) is a pivotal signaling molecule in both the brain and the heart. In this issue of Cell, Erickson et al. (2008) demonstrate a mechanism for CaMKII activation by reactive oxygen species that provides a direct link between kinase activation and cardiac dysfunction.     

Nematode development: new tricks for old genes

The evolution of novel features requires evolutionary change in gene function. New work in nematodes shows how conserved genes can nonetheless contribute to innovative traits.     

Biofilms: new ideas for an old problem

Microbial cells, under moist conditions, are able to adhere to surfaces and to form structured communities embedded in a matrix of extracellular polymeric substances (EPS). In industrial environments, biofilms can cause heat and mass transfer limitations whilst in medical facilities they can be a source of contamination and proliferation of infections. Biofilm formation is related to the pathogenicity of some bacterial strains and cells in biofilms are usually resistant to antimicrobials agents, which increases the interest in new and sound methods for their prevention and destruction.     

Digitalis: new actions for an old drug

The mechanisms by which digitalis causes its therapeutic and toxic actions have been studied for nearly a half century, revealing a great deal about cardiac cell regulation of intracellular ions via the Na-K-ATPase (NKA) and how it is altered by cardiac glycosides. However, recent observations suggest that digitalis may have additional effects on cardiac cell function in both the short and long term that include intracellular effects, interactions with specific NKA isoforms in different cellular locations, effects on intracellular (including nuclear) signaling, and long-term regulation of intracellular ionic balances through circulating ouabain-like compounds. The purpose of this review is to examine the current status of a number of the newest and most interesting developments in the study of digitalis with a particular focus on cardiac function, although we will also discuss some of the new advances in other relevant cardiovascular effects. This new information has important implications for both our understanding of ionic regulation in normal and diseased hearts as well as for potential avenues for the development of future therapeutic interventions for the treatment of heart failure.     

Fruit development: new directions for an old pathway

A recent study investigating the molecular mechanisms of seed pod shattering has shown that the basic helix-loop-helix (bHLH) proteins INDEHISCENT and?ALCATRAZ appear to regulate fruit patterning through gibberellic acid (GA)-DELLA signalling, revealing a central role for bHLH family members in GA?response specificity.     

Metabolic gradients: a new system for old questions

Metabolic gradients are likely to be crucial to normal and abnormal development of cells and tissues. As shown by a new study, a Xenopus egg model system has great promise to illuminate quantitative measures of metabolic gradients in living cytoplasm.     

Mammalian development: new trick for an old dog

A recent study has shown that the T-box gene eomesodermin, which was first identified in Xenopus, not only plays a conserved role in vertebrates directing gastrulation, but interestingly in mammals has acquired a new function in the development of the trophoblast.     

Taurine: new implications for an old amino acid

We describe here a technique for allelic exchange in Francisella tularensis subsp. novicida utilizing polymerase chain reaction (PCR) products. Linear PCR fragments containing gene deletions with an erythromycin resistance cassette insertion were transformed into F. tularensis. The subsequent ErmR progeny were found to have undergone allelic exchange at the correct location in the genome; the minimum flanking homology necessary was 500 bp. This technique was used to create mglA, iglC, bla, and tul4 mutants in F. tularensis subsp. novicida strains. The mglA and iglC mutants were defective for intramacrophage growth, and the tul4 mutant lacked detectable Tul4 by Western immunoblot, as expected. Interestingly, the bla mutant maintained resistance to ampicillin, indicating the presence of multiple ampicillin resistance genes in F. tularensis.     

Rigid linkers for bioactive peptides

Rigid linkers of variable length were used to connect two high-affinity Nle4-D-Phe7-alpha-melanocyte stimulating hormone (NDP-alpha-MSH) or two low-affinity MSH(4) ligands. The linked peptides were synthesized by solid-phase methods. Control experiments indicate there is little or no effect of these linkers on NDP-alpha-MSH or MSH(4) binding to the human melanocortin 4 receptor (hMC4R). Tethering two high-affinity ligands gave no binding enhancement, while tethering two low-affinity ligands resulted in binding enhancement that decreased with increased linker length. Furthermore, for the low-affinity ligands, the enhancement of affinity is inversely proportional to the estimated molecular moments of inertia. These results are consistent with a model wherein binding is enhanced when the rate of ligand reattachment to the receptor is fast relative to the rate of ligand diffusion.     

Veterinary anthelmintics: old and new

Between 1960 and 1980, extraordinary success was achieved in anthelmintic development for animals. In these 20 years, drugs with diverse structure, novel activity and enviable safety were produced for a global livestock industry leading to the productivity gains needed to support a human population that grew by 1.5 billion during the same period. The following 20 years have been spent refining existing molecules with niche activity (parasite and host specificity), improving delivery systems and worrying about the inexorable spread of drug resistance. The challenge for the next 20 years will be to use the technologies available to design and produce new drugs and biological controls. Then, to use the lessons of the past to ensure that the new drugs enjoy a longer useful lifespan and contribute to an animal health industry (livestock and companion) which enriches the lives of a global population. Old and new veterinary anthelmintics comprise a very large field, which could not be comprehensively reviewed in a short article. The present mini-review focuses on major chemical discoveries, formulation developments, administration strategies and new products.