Transcriptional noise adjusted for expression levels reveals genes with high transcriptional noise that are highly expressed, functionally related, and co-regulated in yeast.

Understanding the relationship between variability in single-cell and non-single-cell gene expression studies will aid in understanding the role of and mechanisms that lead to variability in biological systems. Studies on the variation of gene expression levels in yeast normally focus on single cells and use the coefficient of variance (CV) as a measure of noise. The CV is typically negatively correlated with gene expression levels, so most of the studies using yeast find that genes with high transcriptional noise are lowly expressed.

The Influence of Codon Usage, Protein Abundance, and Protein Stability on Protein Evolution Vary by Evolutionary Distance and the Type of Protein.

In general, the evolutionary rate of proteins is not primarily related to protein and amino acid functions, and factors such as protein abundance, codon usage, and the protein's T are more important. To better understand the factors that affect protein evolution, E. coli MG1655 orthologs were compared to those in closely related bacteria and to more distantly related prokaryotes, eukaryotes, and archaea.

Solving the Problem of Assessing Synergy and Antagonism for Non-Traditional Dosing Curve Compounds Using the DE/ZI Method: Application to Nrf2 Activators.

Multi-drug combination therapy carries significant promise for pharmacological intervention, primarily better efficacy with less toxicity and fewer side effects. However, the field lacks methodology to assess synergistic or antagonistic interactions for drugs with non-traditional dose response curves. Specifically, our goal was to assess small-molecule modulators of antioxidant response element (ARE)-driven gene expression, which is largely regulated by the Nrf2 transcription factor.

The evolution of metabolic enzymes in Plasmodium and trypanosomatids as compared to Saccharomyces and Schizosaccharomyces.

Understanding how the biological connectivity of genes and gene products affects evolution is an important aspect of understanding evolution. Genes encoding enzymes are frequently used to carry out such analyses. Interestingly, studies have shown that connectivity in the metabolic networks in parasitic protists, including Plasmodium falciparum and Trypanosoma brucei, have been substantially altered as compared to free living eukaryotes, such as Saccharomyces cerevisiae.

The effects of combinatorial treatments with stress inducing molecules on growth of E. coli colonies.

Stress inducing molecules affect both the mean behavior of bacterial growth and also variations in the growth. While the mechanisms that cause changes in the mean behavior are well understood, little is known about changes in the variation of the population. A true understanding of how organisms respond to stress must include an understanding of the mechanisms and purposes of changes in variation and the distribution not directly related to changes in the mean of the population.

Amino acid biases in the N- and C-termini of proteins are evolutionarily conserved and are conserved between functionally related proteins.

Analysis of the Arabidopsis thaliana, Saccharomyces cerevisiae, Mus musculus, Escherichia coli, Bacillus subtilis, Thermoplasma acidophilum, and Sulfolobus tokodaii genomes demonstrate that many amino acid biases occur at the N- and C-termini of proteins, a statistically significant number of these biases are evolutionarily conserved, and these biases occur in amino acids beyond the first and last five amino acids. Analyses designed to shed light on the mechanism causing amino acid biases suggest that in at least some cases the bias is caused by forces acting at the nucleic acid level. It is also demonstrated that in E.

Identification of a 150 bp cis-acting element of the AtNRT2.1 promoter involved in the regulation of gene expression by the N and C status of the plant.

The Arabidopsis thaliana AtNRT2.1 gene, which encodes a NO(3)(-) transporter involved in high-affinity uptake by the roots, is a molecular target of several mechanisms responsible for the regulation of root NO(3)(-) acquisition by the N status of the plant. All levels of AtNRT2.

A divergent transcription factor TFIIB in trypanosomes is required for RNA polymerase II-dependent spliced leader RNA transcription and cell viability.

Transcription by RNA polymerase II in trypanosomes deviates from the standard eukaryotic paradigm. Genes are transcribed polycistronically and subsequently cleaved into functional mRNAs, requiring trans splicing of a capped 39-nucleotide leader RNA derived from a short transcript, the spliced leader (SL) RNA. The only identified trypanosome RNA polymerase II promoter is that of the SL RNA gene.

Genome-wide patterns of carbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen (CN)-signaling hypothesis in plants.

Background: Carbon and nitrogen are two signals that influence plant growth and development. It is known that carbon- and nitrogen-signaling pathways influence one another to affect gene expression, but little is known about which genes are regulated by interactions between carbon and nitrogen signaling or the mechanisms by which the different pathways interact.

Results: Microarray analysis was used to study global changes in mRNA levels due to carbon and nitrogen in Arabidopsis thaliana.

Genome-wide investigation of light and carbon signaling interactions in Arabidopsis.

Background: Light and carbon are two essential signals influencing plant growth and development. Little is known about how carbon and light signaling pathways intersect or influence one another to affect gene expression.

Results: Microarrays are used to investigate carbon and light signaling interactions at a genome-wide level in Arabidopsis thaliana.

Expressed sequence tag analysis in Cycas, the most primitive living seed plant.

Background: Cycads are ancient seed plants (living fossils) with origins in the Paleozoic. Cycads are sometimes considered a 'missing link' as they exhibit characteristics intermediate between vascular non-seed plants and the more derived seed plants. Cycads have also been implicated as the source of 'Guam's dementia', possibly due to the production of S(+)-beta-methyl-alpha, beta-diaminopropionic acid (BMAA), which is an agonist of animal glutamate receptors.

A paradigm for biological sulfur transfers via persulfide groups: a persulfide-disulfide-thiol cycle in 4-thiouridine biosynthesis.

In support of the key features of sulfur transfer in the proposed mechanisms of 4-thiouridine generation, the enzyme ThiI can turn over only once in the absence of reductants of disulfide bonds, and Cys-456 of ThiI receives the sulfur transferred from the persulfide group of the sulfurtransferase IscS.