The power of now: brief mindfulness induction led to increased randomness of clicking sequence.

The capacity for random movement production is known to be limited in humans (e.g., Newell, Deutsch, & Morrison, 2000). We examined the effects of a brief mindfulness induction on random movement production because there are useful implications for variability in solving movement-related problems. The main task involved randomly clicking the 9 boxes in a 3 × 3 grid presented on a computer screen for five minutes. We characterized the sequence of clicking in terms of degrees of randomness, or periodicity, based on the fit, or probability, of the experimental data with its best fitting Bayesian network (4-click memory nodes) using the Markov chain Monte Carlo (MCMC) approach. Sixty-three participants were randomly assigned to either the experimental or the control condition. Mixed design repeated-measures ANOVA results show that the short mindfulness induction had a positive effect on the randomness of the sequence subsequently produced. This finding suggests that mindfulness may be a suitable strategy for increasing random movement behavior.

Detecting robust time-delayed regulation in Mycobacterium tuberculosis.

BACKGROUND: Time delays are often found in gene regulation though most techniques of building gene regulatory networks are not capable of capturing such phenomena. Here we look at the delays in the DNA repair system of Mycobacterium tuberculosis which is unusually slow in the bacteria. We propose a method based on a skip-chain model to study this phenomena in gene networks. The Viterbi paths of the underlying Markov chains find the most likely regulatory interactions among genes, taking care of very long delays. Using the derived networks, we discuss the delayed regulations and robustness of the DNA damage seen in the bacterium. RESULTS: We evaluated our method on time-course gene expressions after DNA damage with Mitocyin C. Several time-delayed interactions were observed with our analysis. The presence of hubs in the networks indicates that a small number of transcriptional factors regulate the rest of the system. We demonstrate the use of priors to overcome over-fitting problem in the generation of networks. We compare our results with the gene networks derived with dynamic Bayesian networks (DBN). CONCLUSION: Different transcription networks are active at different stages, and constant feedback and regulation is maintained throughout the activities of a biological pathway. Skip-chain models are capable of capturing, long distant and the time-delayed regulations. Use of a Dirichlet prior over parameters and Gibbs prior over structure can greatly reduce the over-fitting in the new model.

Mammalian specific mouse genes are evolving faster than mouse genes conserved across other eukaryotic lineages.

Positive selection is usually considered in the context of a higher rate of substitutions in non-synonymous as compared to synonymous sites in complete coding sequences of genes or individual positions. We show that genes conserved in eukaryota, coelomata, and bilateria, that is, proteins that arose earlier in evolution as compared to mammalia specific genes evolve slowly and are subjected to negative selection. This finding supports the notion that evolutionary rates progressively diminish with the age of a gene. The data suggests that in both intron-containing and intronless genes synonymous sites may be subject to some degree of selection that is indicative of a relative acceleration of amino-acid substitution, which could be due to a relaxation of functional constraints and/or directional selection.

Computational prediction of SEG (single exon gene) function in humans.

Human genes are often interrupted by non-coding, intragenic sequences called introns. Hence, the gene sequence is divided into exons (coding segments) and introns (non-coding segments). Consequently, a majority of them are multi exon genes (MEG). However, a considerable amount of single exon genes (SEG) are present in the human genome (approximately 12%). This amount is sizeable and it is important to probe their molecular function and cellular role. Hence, we performed a genome wide functional assignment to 3750 SEG sequences using PFAM (protein family database), PROSITE (database of biologically meaningful signatures or motifs) and SUPERFAMILY (a library covering all proteins of known 3 dimensional structure). PFAM assigned 13% SEG to trans-membrane receptor genes of the G-protein coupled receptor (GPCR) family and showed that a majority of SEG proteins have DNA binding function. PROSITE identified 336 unique motif types in them and this accounts for 25% of all known patterns, with a majority having PHOSPHORYLATION and ACETYLATION signals. SUPERFAMILY assigned 33% SEG to the membrane all alpha (proteins containing alpha helix structural elements according to SCOP (structural classification of proteins) definition). Functional assignment of SEG proteins at multiple levels (sequence signals, sequence families, 3D structures) using PFAM, PROSITE and SUPERFAMILY is envisioned to suggest their selective and predominant molecular function in cellular systems. Their function as DNA binding, phosphorylating, acetylating and house-keeping agents is intriguing. The analysis also showed evidence of SEG expression and retro-transposition. However, this information is inadequate to draw concerted conclusion on the prevalent role played by these proteins in cellular biology. A complete understanding of SEG function will help to explore their role in cellular environment. The derived datasets from these analyses are available at http://sege.ntu.edu.sg/wester/intronless/human/.

u-Genome: a database on genome design in unicellular genomes.

Unicellular eukaryotes were among the first ones to be selected for complete genome sequencing because of the small size of their genomes and their interactions with humans and a broad range of animals and plants. Currently, ten completely sequenced unicellular genome sequences have been publicly released and as the number of available unicellular genomes increases, comparative genomics analysis within this group of organisms becomes more and more instructive. However, such an analysis is difficult to carry out without a suitable platform gathering not only the original annotations but also relevant information available in public databases or obtained by applying common bioinformatics methods. With the aim of solving these difficulties, we have developed a web-accessible database named u-Genome, the unicellular genome design database. The database is unique in featuring three datasets namely (1) orthologous proteins (2) paralogous proteins and (3) statistical distributions on exons, introns, intergenic DNA and correlations between them. A tool, Uniview, designed to visualize the gene structures for individual genes in the genome is also integrated. This database is of importance in understanding unicellular genome design and architecture and evolution related studies. The database is available through a web interface at http://sege.ntu.edu.sg/wester/ugenome.

Can ends justify the means? Digging deep for human fusion genes of prokaryotic origin.

Gene fusion has been described as an important evolutionary phenomenon. This report focuses on identifying, analyzing, and tabulating human fusion proteins of prokaryotic origin. These fusion proteins are found to mimic operons, simulate protein-protein interfaces in prokaryotes, exhibiting multiple functions and alternative splicing in humans. The accredited biological functions for each of these proteins is made available as a database at http://sege.ntu.edu.sg/wester/fusion/

A report on single exon genes (SEG) in eukaryotes.

Single exon genes (SEG) are archetypical of prokaryotes. Hence, their presence in intron-rich, multi-cellular eukaryotic genomes is perplexing. Consequently, a study on SEG origin and evolution is important. Towards this goal, we took the first initiative of identifying and counting SEG in nine completely sequenced eukaryotic organisms--four of which are unicellular (E. cuniculi, S. cerevisiae, S. pombe, P. falciparum) and five of which are multi-cellular (C. elegans, A. thaliana, D. melanogaster, M. musculus, H. sapiens). This exercise enabled us to compare their proportion in unicellular and multi-cellular genomes. The comparison suggests that the SEG fraction decreases with gene count (r = -0.80) and increases with gene density (r = 0.88) in these genomes. We also examined the distribution patterns of their protein lengths in different genomes.