K-ary clustering with optimal leaf ordering for gene expression data

MOTIVATION: A major challenge in gene expression analysis is effective data organization and visualization. One of the most popular tools for this task is hierarchical clustering. Hierarchical clustering allows a user to view relationships in scales ranging from single genes to large sets of genes, while at the same time providing a global view of the expression data. However, hierarchical clustering is very sensitive to noise, it usually lacks of a method to actually identify distinct clusters, and produces a large number of possible leaf orderings of the hierarchical clustering tree. In this paper we propose a new hierarchical clustering algorithm which reduces susceptibility to noise, permits up to k siblings to be directly related, and provides a single optimal order for the resulting tree. RESULTS: We present an algorithm that efficiently constructs a k-ary tree, where each node can have up to k children, and then optimally orders the leaves of that tree. By combining k clusters at each step our algorithm becomes more robust against noise and missing values. By optimally ordering the leaves of the resulting tree we maintain the pairwise relationships that appear in the original method, without sacrificing the robustness. Our k-ary construction algorithm runs in O(n(3)) regardless of k and our ordering algorithm runs in O(4(k)n(3)). We present several examples that show that our k-ary clustering algorithm achieves results that are superior to the binary tree results in both global presentation and cluster identification. AVAILABILITY: We have implemented the above algorithms in C++ on the Linux operating system.     

Stability and amino acid preferences of type VIII reverse turn: the most common turn in peptides?

Free energies of the alpha(r)beta and betabeta conformations of 14 tetrapeptides, based on the sequence SALN and protein X-ray structures, were calculated using molecular dynamics simulations and MM-PBSA calculations. The alphaalpha conformations of five of the tetrapeptides were also studied. SALN has been earlier shown by molecular dynamics simulations and NMR spectroscopy to have a tendency to form an alpha(r)beta turn. The gas-phase energy of the molecular mechanical force field (CHARMM), the electrostatic and non-polar solvation free energies and solute entropies were used to explain the free energy differences of the alphaalpha, betabeta and alpha(r)beta conformations of the peptides. The alpha(r)beta conformation of SALN and SATN was predicted to be slightly more stable than the extended conformation (betabeta), in agreement with experimental results. The SALN mutants SAIN, SAVN, SATN, SSIN and MSHV, were also predicted to be potential alpha(r)beta turn-forming peptides. We report also revised positional potentials for the type VIII turn, based on a non-homologous set of protein structures. This protein databank analysis confirms the main results of the earlier analyses and reveals several new amino acid residues with a significant positional preference. The results of this work led us to suggest that the alpha(r)beta turn may be the most common turn type in peptides. Such turns may be readily formed in aqueous solution and thereby play important roles in the protein folding process by serving as an initiation point for structure formation.     

Integrin alpha v beta 6 is an RGD-dependent receptor for coxsackievirus A9

Coxsackievirus A9 (CAV9), a member of the Enterovirus genus of Picornaviridae, is a common human pathogen and is one of a significant number of viruses containing a functional arginine-glycine-aspartic acid (RGD) motif in one of their capsid proteins. Previous studies identified the RGD-recognizing integrin alpha(v)beta(3) as its cellular receptor. However, integrin alpha(v)beta(6) has been shown to be an efficient receptor for another RGD-containing picornavirus, foot-and-mouth disease virus (FMDV). In view of the similarity in sequence context of the RGD motifs in CAV9 and FMDV, we investigated whether alpha(v)beta(6) can also serve as a receptor for CAV9. We found that CAV9 can bind to purified alpha(v)beta(6) and also to SW480 cells transfected with beta(6) cDNA, allowing expression of alpha(v)beta(6) on their surface, but it cannot bind to mock-transfected cells. In addition, a higher yield of CAV9 was obtained in beta(6)-expressing cells than in mock-transfected cells. There was no similar enhancement in infection with an RGD-less CAV9 mutant. We also found beta(6) on the surface of GMK cells, a cell line which CAV9 infects efficiently by an RGD-dependent mechanism. Significantly, this infection is blocked by an antibody to alpha(v)beta(6), while this antibody did not block the low level of infection by the RGD-less mutant. Thus, integrin alpha(v)beta(6) is an RGD-dependent receptor for CAV9 and may be important in natural CAV9 infections.     

Influence of Pb contamination in boreal forest soil on the growth and ligninolytic activity of litter-decomposing fungi

Lignin mineralization activity of three basidiomycetous litter-decomposing fungi (LDF) was studied with humus layer samples taken from a boreal forest soil. The total Pb concentration in the samples was 32,000 mg kg(-1) and water soluble Pb 67 mg kg(-1). Synthetic lignin mineralization by Collybia dryophila and Clitocybe (Lepista) nebularis was strongly inhibited, whereas Stropharia coronilla was more tolerant to Pb stress in soil and liquid cultures. Purified laccases maintained their activity and purified MnPs remained partly active up to a concentration of 1450 mg Pb l(-1). High concentrations of Pb inhibited the growth of LDF and affected the activity of ligninolytic enzymes, but the extent of inhibition varied among different LDF species. In consequence, Pb contamination in soil may have a negative impact on recycling of organic carbon.     

Dynamic covariation between gene expression and proteome characteristics

Background  

Cells react to changing intra- and extracellular signals by dynamically modulating complex biochemical networks. Cellular responses to extracellular signals lead to changes in gene and protein expression. Since the majority of genes encode proteins, we investigated possible correlations between protein parameters and gene expression patterns to identify proteome-wide characteristics indicative of trends common to expressed proteins.     

Thermoregulatory adaptations of the overwintering captive raccoon dog (Nyctereutes procyonoides) in boreal climate

The raccoon dog (Nyctereutes procyonoides) is a nocturnal canid thought to utilise passive wintering strategy in the boreal climate. To record the deep body temperature (T(b)), 12 farmed raccoon dogs were implanted with intra-abdominal T(b) loggers on November 26, 2003. Between December 3, 2003 and January 27, 2004 half of the animals were fasted for 8 weeks. The amplitude of the diurnal T(b) oscillations increased due to fasting. However, the mean diurnal T(b) was lower in the fasted animals only during two occasions. Unlike observed previously in other species, not only did the raccoon dogs experience hypothermia between 0600 and 1000 hr but also hyperthermia between noon and 1800 hr. The fasted animals were as active as the fed animals measured after 42-43 days of fasting and there was a significant cross-correlation between physical activity and T(b). The nocturnal period of hypothermia is probably an adaptation to save energy during food deprivation. The diurnal hyperthermia could be explained by the opportunistic foraging behaviour of the species. Opposite to the established assumptions, the raccoon dog does not seem to enter winter sleep on fur farms. In the future it is important to determine if true winter sleep occurs in nature in the species.     

The structure of Neurospora crassa 3-carboxy-cis,cis-muconate lactonizing enzyme, a beta propeller cycloisomerase

Muconate lactonizing enzymes (MLEs) convert cis,cis-muconates to muconolactones in microbes as part of the beta-ketoadipate pathway; some also dehalogenate muconate derivatives of xenobiotic haloaromatics. There are three different MLE classes unrelated by evolution. We present the X-ray structure of a eukaryotic MLE, Neurospora crassa 3-carboxy-cis,cis-muconate lactonizing enzyme (NcCMLE) at 2.5 A resolution, with a seven-bladed beta propeller fold. It is related neither to bacterial MLEs nor to other beta propeller enzymes, but is structurally similar to the G protein beta subunit. It reveals a novel metal-independent cycloisomerase motif unlike the bacterial metal cofactor MLEs. Together, the bacterial MLEs and NcCMLE structures comprise a striking structural example of functional convergence in enzymes for 1,2-addition-elimination of carboxylic acids. NcCMLE and bacterial MLEs may enhance the reaction rate differently: the former by electrophilic catalysis and the latter by electrostatic stabilization of the enolate.     

Physiology and taxonomy of thiobacillus strain TJ330, which oxidizes carbon disulphide (CS2)

A bacterium (strain TJ330) capable of using carbon disulphide (CS2) as its sole energy source in an acidic environment was isolated from a peat biofilter used in experiments to remove CS2 and hydrogen sulphide (H2S) from air. Its physiology and taxonomy are described here. The strain oxidized CS2, H2S and elemental sulphur to sulphate chemolithotrophically. The rate of sulphate production was highest at pH 2. The maximum growth rate constant (micromax) using CS2 as a substrate was 3.9 x 10(-2) h(-1) (generation time 18 h) and the Monod constant (Ks) was 0.97-2.6 micromol l(-1) CS2 (74-198 microg l(-1)), corresponding to an equilibrium with 15-40 ppm CS2 in the headspace. The optimum growth temperature using elemental sulphur as a substrate was 28 degrees C. The strain bears morphological and physiological similarities to Thiobacillus thiooxidans, but the latter is incapable of oxidizing CS2. The strain TJ330 (DSM 8985) showed only 44.2 + 11.8% DNA homology with the type strain T. thiooxidans ATCC 19377, while its homology with T. ferrooxidans ATCC 23270 was 17.1 + 3.4%. The strain TJ 330 represents a high-affinity bacterium which can effectively remove low CS2 concentrations in an acid environment. These properties can be utilized in biotechnological purification applications.     

Seasonal rhythms of body temperature in the free-ranging raccoon dog (Nyctereutes procyonoides) with special emphasis on winter sleep

The raccoon dog (Nyctereutes procyonoides) is the only canid with passive overwintering in areas with cold winters, but the depth and rhythmicity of wintertime hypothermia in the wild raccoon dog are unknown. To study the seasonal rhythms of body temperature (T(b)), seven free-ranging animals were captured and implanted with intra-abdominal T(b) loggers and radio-tracked during years 2004-2006. The average size of the home ranges was 306+/-26 ha, and the average 24 h T(b) was 38.0+/-<0.01 degrees C during the snow-free period (May-November). The highest and lowest T(b) were usually recorded around midnight (21:00-02:00 h) and between 05:00-11:00 h, respectively, and the range of the 24 h oscillations was 1.2+/-0.01 degrees C. The animals lost approximately 43+/-6% of body mass in winter (December-April), when the average size of the home ranges was 372+/-108 ha. During the 2-9-wk periods of passivity in January-March, the average 24 h T(b) decreased by 1.4-2.1 degrees C compared to the snow-free period. The raccoon dogs were hypothermic for 5 h in the morning (06:00-11:00 h), whereas the highest T(b) values were recorded between 16:00-23:00 h. The range of the 24 h oscillations increased by approximately 0.6 degrees C, and the rhythmicity was more pronounced than in the snow-free period. The ambient temperature and depth of snow cover were important determinants of the seasonal T(b) rhythms. The overwintering strategy of the raccoon dog resembled the patterns of winter sleep in bears and badgers, but the wintertime passivity of the species was more intermittent and the decrease in the T(b) less pronounced.