538 research outputs found
Turbulence near cyclic fold bifurcations in birhythmic media
We show that at the onset of a cyclic fold bifurcation, a birhythmic medium
composed of glycolytic oscillators displays turbulent dynamics. By computing
the largest Lyapunov exponent, the spatial correlation function, and the
average transient lifetime, we classify it as a weak turbulence with transient
nature. Virtual heterogeneities generating unstable fast oscillations are the
mechanism of the transient turbulence. In the presence of wavenumber
instability, unstable oscillations can be reinjected leading to stationary
turbulence. We also find similar turbulence in a cell cycle model. These
findings suggest that weak turbulence may be universal in biochemical
birhythmic media exhibiting cyclic fold bifurcations.Comment: 14 pages 10 figure
Symmetry-breaking in chiral polymerisation
We propose a model for chiral polymerisation and investigate its symmetric
and asymmetric solutions. The model has a source species which decays into
left- and right-handed types of monomer, each of which can polymerise to form
homochiral chains; these chains are susceptible to `poisoning' by the opposite
handed monomer. Homochiral polymers are assumed to influence the proportion of
each type of monomer formed from the precursor. We show that for certain
parameter values a positive feedback mechanism makes the symmetric steady-state
solution unstable. The kinetics of polymer formation are then analysed in the
case where the system starts from zero concentrations of monomer and chains. We
show that following a long induction time, extremely large concentrations of
polymers are formed for a short time, during this time an asymmetry introduced
into the system by a random external perturbation may be massively amplified.
The system then approaches one of the steady-state solutions described above.Comment: 26pages, 6 Figure
A rapid assay for affinity and kinetics of molecular interactions with nucleic acids
The Differential Radial Capillary Action of Ligand Assay (DRaCALA) allows detection of protein interactions with low-molecular weight ligands based on separation of the proteināligand complex by differential capillary action. Here, we present an application of DRaCALA to the study of nucleic acidāprotein interactions using the Escherichia coli cyclic AMP receptor protein (CRP). CRP bound in DRaCALA specifically to 32P-labeled oligonucleotides containing the consensus CRP binding site, but not to oligonucleotides with point mutations known to abrogate binding. Affinity and kinetic studies using DRaCALA yielded a dissociation constant and dissociation rate similar to previously reported values. Because DRaCALA is not subject to ligand size restrictions, whole plasmids with a single CRP-binding site were used as probes, yielding similar results. DNA can also function as an easily labeled carrier molecule for a conjugated ligand. Sequestration of biotinylated nucleic acids by streptavidin allowed nucleic acids to take the place of the protein as the immobile binding partner. Therefore, any molecular interactions involving nucleic acids can be tested. We demonstrate this principle utilizing a bacterial riboswitch that binds cyclic-di-guanosine monophosphate. DRaCALA is a flexible and complementary approach to other biochemical methods for rapid and accurate measurements of affinity and kinetics at near-equilibrium conditions
Minigene-like inhibition of protein synthesis mediated by hungry codons near the start codon
Rare AGA or AGG codons close to the initiation codon inhibit protein synthesis by a tRNA-sequestering mechanism as toxic minigenes do. To further understand this mechanism, a parallel analysis of protein synthesis and peptidyl-tRNA accumulation was performed using both a set of lacZ constructs where AGAAGA codons were moved codon by codon from +2, +3 up to +7, +8 positions and a series of 3ā8 codon minigenes containing AGAAGA codons before the stop codon. Ī²-Galactosidase synthesis from the AGAAGA lacZ constructs (in a Pth defective in vitro system without exogenous tRNA) diminished as the AGAAGA codons were closer to AUG codon. Likewise, Ī²-galactosidase expression from the reporter +7 AGA lacZ gene (plus tRNA, 0.25 Ī¼g/Ī¼l) waned as the AGAAGAUAA minigene shortened. Pth counteracted both the length-dependent minigene effect on the expression of Ī²-galactosidase from the +7 AGA lacZ reporter gene and the positional effect from the AGAAGA lacZ constructs. The +2, +3 AGAAGA lacZ construct and the shortest +2, +3 AGAAGAUAA minigene accumulated the highest percentage of peptidyl-tRNAArg4. These observations lead us to propose that hungry codons at early positions, albeit with less strength, inhibit protein synthesis by a minigene-like mechanism involving accumulation of peptidyl-tRNA
Biocatalytic Synthesis of Polymers of Precisely Defined Structures
The fabrication of functional nanoscale devices requires the construction of complex architectures at length scales characteristic of atoms and molecules. Currently microlithography and micro-machining of macroscopic objects are the preferred methods for construction of small devices, but these methods are limited to the micron scale. An intriguing approach to nanoscale fabrication involves the association of individual molecular components into the desired architectures by supramolecular assembly. This process requires the precise specification of intermolecular interactions, which in turn requires precise control of molecular structure
Novel Roles of cAMP Receptor Protein (CRP) in Regulation of Transport and Metabolism of Carbon Sources
CRP (cAMP receptor protein), the global regulator of genes for carbon source utilization in the absence of glucose, is the best-studied prokaryotic transcription factor. A total of 195 target promoters on the Escherichia coli genome have been proposed to be under the control of cAMP-bound CRP. Using the newly developed Genomic SELEX screening system of transcription factor-binding sequences, however, we have identified a total of at least 254 CRP-binding sites. Based on their location on the E. coli genome, we predict a total of at least 183 novel regulation target operons, altogether with the 195 hitherto known targets, reaching to the minimum of 378 promoters as the regulation targets of cAMP-CRP. All the promoters selected from the newly identified targets and examined by using the lacZ reporter assay were found to be under the control of CRP, indicating that the Genomic SELEX screening allowed to identify the CRP targets with high accuracy. Based on the functions of novel target genes, we conclude that CRP plays a key regulatory role in the whole processes from the selective transport of carbon sources, the glycolysis-gluconeogenesis switching to the metabolisms downstream of glycolysis, including tricarboxylic acid (TCA) cycle, pyruvate dehydrogenase (PDH) pathway and aerobic respiration. One unique regulation mode is that a single and the same CRP molecule bound within intergenic regions often regulates both of divergently transcribed operons
- ā¦