Transcription factor binding site identification using the self-organizing map

MOTIVATION: The automatic identification of over-represented motifs present in a collection of sequences continues to be a challenging problem in computational biology. In this paper, we propose a self-organizing map of position weight matrices as an alternative method for motif discovery. The advantage of this approach is that it can be used to simultaneously characterize every feature present in the dataset, thus lessening the chance that weaker signals will be missed. Features identified are ranked in terms of over-representation relative to a background model. RESULTS: We present an implementation of this approach, named SOMBRERO (self-organizing map for biological regulatory element recognition and ordering), which is capable of discovering multiple distinct motifs present in a single dataset. Demonstrated here are the advantages of our approach on various datasets and SOMBRERO's improved performance over two popular motif-finding programs, MEME and AlignACE. AVAILABILITY: SOMBRERO is available free of charge from http://bioinf.nuigalway.ie/sombrero SUPPLEMENTARY INFORMATION: http://bioinf.nuigalway.ie/sombrero/additional.     

Dramatic age-related changes in nuclear and genome copy number in the nematode Caenorhabditis elegans

The nematode Caenorhabditis elegans has become one of the most widely used model systems for the study of aging, yet very little is known about how C. elegans age. The development of the worm, from egg to young adult has been completely mapped at the cellular level, but such detailed studies have not been extended throughout the adult lifespan. Numerous single gene mutations, drug treatments and environmental manipulations have been found to extend worm lifespan. To interpret the mechanism of action of such aging interventions, studies to characterize normal worm aging, similar to those used to study worm development are necessary. We have used 4',6'-diamidino-2-phenylindole hydrochloride staining and quantitative polymerase chain reaction to investigate the integrity of nuclei and quantify the nuclear genome copy number of C. elegans with age. We report both systematic loss of nuclei or nuclear DNA, as well as dramatic age-related changes in nuclear genome copy number. These changes are delayed or attenuated in long-lived daf-2 mutants. We propose that these changes are important pathobiological characteristics of aging nematodes.     

Description of Meloidogyne nataliei n. sp. (Nematoda: Meloidogynidae) from Grape (Vitis labrusca) in Michigan,with SEM Observations

Meloidogyne nataliei n. sp. is described and illustrated from grape (Vitis labrusca) in a declining vineyard at Mattawan, Michigan, USA. Infected grape roots exhibit no hyperplastic symptoms. Females protrude from the roots and are surrounded by a massive egg sac containing many eggs. This new species is distinguishable from other species of the genus especially by its large, striking perineal pattern with, usually, two ropelike separated striae on each side extending laterally from the vulval and anal areas. Among other diagnostic characters are the location of the female excretory pore adjacent to or near the base of the head and the heavy larval stylet averaging about 22 μm in length. Examination of males, females, and larvae with the scanning electron microscope confirmed observations made by optical microscopy and revealed diagnostic and other structures in greater detail. Of particular significance was the nature of the male head, with a massive circular labial disc on which is located a rectangular structure surrounding the oral opening, and the six distinct lips appearing as a rosette in en face view. The known distribution of this new species is presently limited to its original location in Michigan.     

The trophic interactions of young Arctic grayling (Thymallus arcticus) in an Arctic tundra stream

1. Young (0+) Arctic grayling (Thymallus arcticus) have the potential to control the trophic structure of Arctic tundra streams through consumption, nutrient excretion and the modification of prey behaviour. The effect of young grayling on three trophic levels (algae, invertebrates and fish) was investigated by manipulating fish density and by fertilizing the river with phosphorus (P). 2. Nutrients, epilithic chlorophyll a, benthic invertebrates and fish biomass were measured within each fish density treatment (0, 4, and 40 fish m^–2) within the P-limited reference zone and the P-enriched fertilized zone of the Kuparuk River, Alaska. 3. Epilithic chlorophyll a increased with increased fish density in both reference and fertilized zones, while mayfly density decreased with increased fish density in the fertilized zone only. Final mean mass of young grayling in the 40 fish m^–2 cages was lower than mean mass in the 4 fish m^–2 cages. 4. Young grayling may produce a top-down cascading trophic effect in areas where nutrients are not limited. 5. River nutrient status and river discharge may modify the strength of top-down control by young grayling.     

Gap junction structures: Analysis of the x-ray diffraction data

Models for the spatial distribution of protein, lipid and water in gap junction structures have been constructed from the results of the analysis of X-ray diffraction data described here and the electron microscope and chemical data presented in the preceding paper (Caspar, D. L. D., D. A. Goodenough, L. Makowski, and W.C. Phillips. 1977. 74:605-628). The continuous intensity distribution on the meridian of the X-ray diffraction pattern was measured, and corrected for the effects of the partially ordered stacking and partial orientation of the junctions in the X-ray specimens. The electron density distribution in the direction perpendicular to the plane of the junction was calculated from the meridional intensity data. Determination of the interference function for the stacking of the junctions improved the accuracy of the electron density profile. The pair-correlation function, which provides information about the packing of junctions in the specimen, was calculated from the interference function. The intensities of the hexagonal lattice reflections on the equator of the X-ray pattern were used in coordination with the electron microscope data to calculate to the two-dimensional electron density projection onto the plane of the membrane. Differences in the structure of the connexons as seen in the meridional profile and equatorial projections were shown to be correlated to changes in lattice constant. The parts of the junction structure which are variable have been distinguished from the invariant parts by comparison of the X-ray data from different specimens. The combination of these results with electron microscope and chemical data provides low resolution three- dimensional representations of the structures of gap junctions.     

Spectral analysis and connectivity of porous microstructures in bone

Cancellous bone is a porous composite of calcified tissue interspersed with soft marrow. Sea ice is also a porous composite, consisting of pure ice with brine, air, and salt inclusions. Interestingly, the microstructures of bone and sea ice exhibit notable similarities. In recent years, we have developed mathematical and experimental techniques for imaging and characterizing the brine microstructure of sea ice, such as its volume fraction and connectivity, as well as a range of theoretical approaches for studying fluid, thermal, and electromagnetic transport in sea ice. Here we explore the application of our sea ice techniques to investigate trabecular bone. For example, percolation theory that quantifies brine connectivity and its thermal evolution can also help assess the impact of osteoporosis on trabecular structure. Central to our approach is the spectral measure of a composite material, which contains detailed information about the mixture geometry, and can be used in powerful integral representations to compute the effective properties. The spectral measure is obtained from the eigenvalues and eigenvectors of a self-adjoint operator determined exclusively by the composite microgeometry. Here we compute the spectral measures for discretizations of images of healthy and osteoporotic bone. The measures are used to compute the effective electromagnetic properties of the bone specimens. These data are then inverted to reconstruct the porosity of the original specimens, with excellent agreement.     

Topography of the neurotensin (NT)(8-9) binding site of human NT receptor-1 probed with NT(8-13) analogs.

A series of neurotensin (NT)(8-13) analogs featuring substitution of the Arg8 and/or Arg9 residues with non-natural cationic amino acids was synthesized and evaluated for binding to the human NT receptor-1 (hNTR-1). The modifications were designed to probe specific steric and electrostatic requirements in the N-terminal cationic region of NT(8-13) for receptor binding as a general evaluation of the feasibility of incorporating minor structural changes into a peptide at a crucial polar receptor binding site. Many of the non-natural amino acids are more or less isosteric to Arg but more lipophilic as a result of addition of alkyl groups or through removal or replacement of NH character with methylene or methyl substituents, whereas others vary the distance between the cation and the alpha-amino acid carbon. Substitution of Arg8 with N(G)-alkylated Arg derivatives or homolysine (Hlys) maintained the subnanomolar affinity of NT(8-13) to the hNTR-1. Position 8 incorporation of Hlys produced the most favorable primary amine side-chain substitution to date. Moderate losses in affinity observed with position 9 substitutions were attributed to adverse steric effects. Doubly substituted [Hlys8, DAB9]NT(8-13), in which DAB is 2,4-diaminobutyric acid, was also prepared and tested as the shorter side-chain of DAB is known to be favored in position 9 of NT(8-13). This analog maintained 60% of NT(8-13) binding affinity making it the most favored des-guanidinium-containing analog known. These results demonstrate that adequate receptor binding affinity can be maintained over a structural range of Arg analogs, thus providing a range of peptides expected to exhibit altered pharmacokinetic properties. From the standpoint of the hNTR-1 cationic binding sites, these results help to map out the structural stringency inherent in the formation of a tight binding complex with NT(8-13) and related analogs.