Base pair selectivity in the binding of copper (II) tetrakis (4-N-methylpyridyl)porphine to polynucleotides under closely packed conditions.

The base pair selectivity of the intercalative binding of the copper porphyrin, copper (II) tetrakis(4-N-methylpyridyl)porphine (Cu(II)TMpyP-4), to DNA has been investigated using a variety of DNA types and the synthetic polynucleotides poly(dG-dC)2 and poly(dA-dT)2. The studies utilize electron paramagnetic resonance of concentrated gels which are thought to mimic the closely packed state of nuclear DNA. The results indicate that intercalation of this porphyrin is preferred for sites containing two adjacent G-C base pairs, irrespective of sequence.     

Carboxypeptidase Activity of the Zinc Metalloprotease in the Cement Precursor Secretion of the Barnacle, Chthamalus fragilis Darwin

The liquid cement precursor secretion (CPS) of the adult barnacle, Chthamalus fragilis, exhibits Zn-metalloprotease activity. To assess the bond specificity of the Zn-metalloprotease, samples of liquid CPS were collected by glass micropipette from the exposed bases of adult barnacles and incubated in 50 mM Tris buffer, pH 8.0, containing 10 mM Ca⁺⁺, at 27°C or 20°C for 6 or 24 hr. in the presence of fluorescent dye-labeled synthetic C-1 and A-1 PepTag peptides. These peptides have a net positive charge and migrate toward the anode during agarose gel electrophoresis. When incubated with the C-1 PepTag peptide, CPS samples generated F1 hydrolysis fragments that failed to migrate during electrophoresis in 0.8% agarose gels, indicating the presence of proteolytic activity in the CPS. Proteolysis of the C-1 peptide was inhibited by 2.0 mM orthophenanthroline in the presence of 10 mM Ca⁺⁺ ions. No hydrolysis products were generated when samples of CPS were incubated in the presence of the A-1 PepTag peptide. This suggested that the CPS contained a Zn-metalloprotease that exhibited a preference for the carboxy-terminal lysine of the C-1 PepTag peptide. There were no indications of aminopeptidase or endopeptidase activities in the barnacle CPS. When incubated with hippuryl-lysine and hippuryl-arginine substrates, samples of CPS gave activities ranging from 111 to 319 μmol hippuric acid formed/min/mg of CPS protein. These observations indicate that the CPS of C. fragilis contains a Zn-metallo-exoprotease with a preference for carboxy-terminal basic amino acids.     

Transposable Element Loads in a Bacterial Symbiont of Weevils Are Extremely Variable

Not only are transposable elements profuse in the bacterial endosymbiont of maize weevils, but we found that their quantities also vary ~10-fold among individual weevils. Because multicopy elements can facilitate homologous recombination, this insertion sequence (IS) load variability suggests that these essentially asexual bacteria may exhibit substantial intraspecific genomic variation.     

ATP promotes the appearance of two DNA-binding forms of the Ah receptor.

Following the binding of a specific ligand such as 2,3,7,8-tetrachlorodibenzo-p-dioxin, mild heating has previously been shown to convert cytosolic aryl hydrocarbon (Ah) receptor to two DNA-binding forms: peak I, which appears to be an Ah receptor monomer; and peak II, which is larger and resembles nuclear Ah receptor. In rat liver cytosol pretreated with charcoal-dextran, and heated briefly at 22 degrees C, the addition of a physiological (3 mM) concentration of ATP substantially increases the formation of both peak I and peak II receptor. On more extended incubation in the presence of ATP most of the Ah receptor converts to the tighter binding peak II form. The ATP analog 5'-adenylylmethylene diphosphonate (AMPPCP) stimulates the appearance of both DNA-binding forms as effectively as ATP does. In cytosol separated from low molecular weight components by gel filtration prior to incubation, ATP substantially stimulates the appearance of peak II receptor. ATP also increases the amount of peak II receptor formed when peak I receptor is incubated with unlabeled charcoal-treated cytosol. Thus, ATP promotes both the release of Ah receptor monomer from the 9 S complex which cannot bind DNA and the subsequent conversion of that monomer to a form similar or identical to nuclear Ah receptor.     

Scalable optimal Bayesian classification of single-cell trajectories under regulatory model uncertainty

Background

Biological networks describes the mechanisms which govern cellular functions. Temporal networks show how these networks evolve over time. Studying the temporal progression of network topologies is of utmost importance since it uncovers how a network evolves and how it resists to external stimuli and internal variations. Two temporal networks have co-evolving subnetworks if the evolving topologies of these subnetworks remain similar to each other as the network topology evolves over a period of time. In this paper, we consider the problem of identifying co-evolving subnetworks given a pair of temporal networks, which aim to capture the evolution of molecules and their interactions over time. Although this problem shares some characteristics of the well-known network alignment problems, it differs from existing network alignment formulations as it seeks a mapping of the two network topologies that is invariant to temporal evolution of the given networks. This is a computationally challenging problem as it requires capturing not only similar topologies between two networks but also their similar evolution patterns.

Results

We present an efficient algorithm, Tempo, for solving identifying co-evolving subnetworks with two given temporal networks. We formally prove the correctness of our method. We experimentally demonstrate that Tempo scales efficiently with the size of network as well as the number of time points, and generates statistically significant alignments—even when evolution rates of given networks are high. Our results on a human aging dataset demonstrate that Tempo identifies novel genes contributing to the progression of Alzheimer’s, Huntington’s and Type II diabetes, while existing methods fail to do so.

Conclusions

Studying temporal networks in general and human aging specifically using Tempo enables us to identify age related genes from non age related genes successfully. More importantly, Tempo takes the network alignment problem one huge step forward by moving beyond the classical static network models.