Importance of data structure in comparing two dimension reduction methods for classification of microarray gene expression data

Background  

With the advance of microarray technology, several methods for gene classification and prognosis have been already designed. However, under various denominations, some of these methods have similar approaches. This study evaluates the influence of gene expression variance structure on the performance of methods that describe the relationship between gene expression levels and a given phenotype through projection of data onto discriminant axes.     

Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88

Elucidating the relationship between sequence and conformation is essential for the understanding of functions of proteins. While sharing 88 % sequence identity and differing by only seven residues, GA88 and GB88 have completely different structures and serve as ideal systems for investigating the relationship between sequence and function. Benefiting from the continuous advancement of the computational ability of modern computers, molecular dynamics (MD) simulation is now playing an increasingly important role in the study of proteins. However, the reliability of MD simulations is limited by the accuracy of the force fields and solvent model approximations. In this work, several AMBER force fields (AMBER03, AMBER99SB, AMBER12SB, AMBER14SB, AMBER96) and solvent models (TIP3P, IGB5, IGB7, IGB8) have been employed in the simulations of GA88 and GB88. The statistical results from 19 simulations show that GA88 and GB88 both adopt more compact structures than the native structures. GB88 is more stable than GA88 regardless of the force fields and solvent models utilized. Most of the simulations overestimated the salt bridge interaction. The combination of AMBER14SB force field and IGB8 solvent model shows the best overall performance in the simulations of both GA88 and GB88. AMBER03 and AMBER12SB also yield reasonable results but only in the TIP3P explicit solvent model.     

The role of bryozoans in fossil reefs—an example from the Middle Devonian of the Western Sahara

Stenolaemate bryozoans with their stable calcitic skeletons play a significant role in reef building. In the Middle Devonian Sabkhat Lafayrina reef complex (Western Sahara), bryozoans are abundant and diverse. Although they do not form part of the principal framework of reefs, bryozoans are involved significantly in reef growth, especially in the initial stage. In this way, bryozoans are important with respect to initiating reef growth. They contribute greatly to sediment stabilization, making it possible for principal reef builders to grow on hardened and stabilized substrates, and also play sediment-baffling and sediment-filling roles. The aim of this study is to document the diversity of bryozoans in a Middle Devonian reef complex and to estimate their potential for initiation and contribution to reef structures.     

Mediatietherapie bij ouderen met een persoonlijkheidsstoornis: Een verpleegkundige benadering

Behavioural counselling by nurses can enhance quality of life in elderly with a personality disorder. Although nurses have a crucial role in day-to-day treatment, there is a lack of evidence-based approaches. Based on the cognitive therapy, the treatment protocol Cognitive Model for Behavioural Interventions (CoMBI) provides an alternative nursing approach for personality disorders.     

Identification and characterization of endoglucanases for fungicidal activity in <Emphasis Type="Italic">Anabaena laxa</Emphasis> (Cyanobacteria)

A cyanobacterial strain (Anabaena laxa RPAN8) exhibiting fungicidal activity and β-1,3 and 1,4 endoglucanase activities was selected for identifying the gene(s) involved. Functional analyses of the genomic library revealed that four clones (8, 64, 116, and 248) of RPAN8 exhibited fungicidal activity and induced structural deformities in the cell wall of the growing mycelia of Pythium aphanidermatum. Higher expression of fungicidal and β-1,4 endoglucanase activities, along with low expression of β-1,3 endoglucanase activity, was recorded in two E. coli clones (8 and 64). Clones 8 and 64 exhibited identical sequences while clones 116 and 248 were also similar. Bioinformatic analyses were undertaken only for the two non-identical clones 8 and 116 which showed open reading frames (ORFs) of 348 (end 1) and 656 amino acid residues (end 2), respectively. The amino acid sequence analyses revealed that the end 1 encoding endoglucanases belonged to peptidase M20 family while end 2 showed significant similarities with several known genes. The putative promoters and ribosomal binding sites were identified and amino acid exchanges were observed in both end 1 and 2. The presence of signal peptides of 24 and 20 amino acid residues respectively revealed the secretory nature of these proteins.     

Proteome-wide evidence for enhanced positive Darwinian selection within intrinsically disordered regions in proteins

Background  

Understanding the adaptive changes that alter the function of proteins during evolution is an important question for biology and medicine. The increasing number of completely sequenced genomes from closely related organisms, as well as individuals within species, facilitates systematic detection of recent selection events by means of comparative genomics.     

Persistence of Dispersal-limited Species in Structured Dynamic Landscapes

Dynamic landscape models have generally assumed random distributions of habitat although real landscapes show spatial organization at many scales. To explore the role of spatial structure in determining the frequency of dispersal-limited forest species, we used a cellular landscape model divided into two zones. Zones were distributed in a random, clustered, or regular spatial pattern. Within each zone habitat cells were randomly destroyed and regenerated, and habitat density and turnover rate were systematically varied. A hypothetical habitat-limited species dispersed between adjacent habitat cells. All trials showed a reduced species frequency relative to a static landscape. Reduction was greater at low habitat density (P = 0.30) than at high density (0.90) suggesting the importance of habitat connectivity in controlling species frequency. The greatest reduction occurred when habitat was concentrated in a small, regularly distributed zone at low habitat density reflecting the enforced isolation of individual habitat cells. Very little reduction was observed when habitat cells were packed into a small clustered zone, a situation promoting connectivity between cells. Moderate–severe frequency reduction occurred when habitat turnover was concentrated in a clustered zone at high habitat density, but little was observed when turnover was widely distributed in a regular or random pattern. These results can be interpreted in terms of a source-sink function in which spatial pattern controlled the degree of contact between landscape zones and determined opportunities for dispersal between habitat cells. We conclude that clustering of forest habitat has the potential to maintain herb species frequency in sparsely forested landscapes. Conversely, clustering of forest disturbance in heavily forested regions, or regular distribution of forest stands (as often occurs in agricultural regions) creates areas which are difficult to colonize, and should be avoided.     

Changes in plant chemical defenses and nutritional quality as a function of ontogeny in <Emphasis Type="Italic">Plantago lanceolata</Emphasis> (Plantaginaceae)

Numerous empirical studies have examined ontogenetic trajectories in plant defenses but only a few have explored the potential mechanisms underlying those patterns. Furthermore, most documented ontogenetic trajectories in plant defenses have generally concentrated on aboveground tissues; thus, our knowledge regarding whole plant trends in plant defenses throughout development or potential allocation constraints between growth and defenses is limited. Here, we document changes in plant biomass, nutritional quality and chemical defenses for below- and aboveground tissues across seven age classes of Plantago lanceolata (Plantaginaceae) to evaluate: (1) partial and whole plant ontogenetic trajectories in constitutive chemical defenses and nutritional quality, and (2) the role of resource allocation constraints, namely root:shoot (R:S) ratios, in explaining whole plant investment in chemical defenses over time. Overall investment in iridoid glycosides (IGs) significantly increased, while water and nitrogen concentrations in shoot tissues decreased with plant age. Significant variation in IG content between shoot and root tissues across development was observed: allocation of IGs into root tissues linearly increased from younger to older plants, while non-linear shifts in allocation of IGs during ontogeny were observed for shoot tissues. Finally, R:S ratios only weakly explained overall allocation of resources into defenses, with young stages showing a positive relationship, while older stages showed a negative relationship between R:S ratios and IG concentrations. Ontogenetic trajectories in plant quality and defenses within and among plant tissues can strongly influence insect herbivores’ performance and/or predation risk; thus, they are likely to play a significant role in mediating species interactions.