Fast optimal genome tiling with applications to microarray design and homology search.

In this paper, we consider several variations of the following basic tiling problem: given a sequence of real numbers with two size-bound parameters, we want to find a set of tiles of maximum total weight such that each tiles satisfies the size bounds. A solution to this problem is important to a number of computational biology applications such as selecting genomic DNA fragments for PCR-based amplicon microarrays and performing homology searches with long sequence queries. Our goal is to design efficient algorithms with linear or near-linear time and space in the normal range of parameter values for these problems. For this purpose, we first discuss the solution to a basic online interval maximum problem via a sliding-window approach and show how to use this solution in a nontrivial manner for many of the tiling problems introduced. We also discuss NP-hardness results and approximation algorithms for generalizing our basic tiling problem to higher dimensions. Finally, computational results from applying our tiling algorithms to genomic sequences of five model eukaryotes are reported.     

Tripeptides as selective inhibitors of src-SH2 phosphoprotein interactions

Summary This paper describes the synthesis of phosphorylated peptides of the general structural Ac-Tyr(PO₃H₂)-Glu-Xaa_NH₂, where Xaa represents a hydrophobic -amino acid of d-configuration. These peptides displayed activities in the micromolar range in inhibiting src-SH2 domain/epidermal growth factor receptor interactions.     

Early agonistic experience and rank acquisition among free-ranging infant rhesus monkeys

Several aspects of agonistic experience are described for freeranging infant rhesus monkeys (Macaca mulatta)on Cayo Santiago. Even before infants are fully integrated with peers in rank dominance based on maternal ranks,infants of highranking mothers tend to be threatened less frequently by other members of the group and are less likely to be threatened by unfamiliar individuals than are infants of lowranking mothers. There is no evidence that fearful interactions between pairs of infants are related to their mother’s ranks before 22 weeks of age. However, an imperfect hierarchy can be constructed for infants between 27 and 30 weeks of age. At this age,infants of higherranking mothers are also more likely to receive protection when threatened than are infants of lowerranking mothers. When protected, their protectors are less likely to emit fearful gestures to the infants’ threatener. Close female relatives appear to play a large role in the protection of infants and may be more directly responsible for the differences described above than the mother, other relatives, or other highranking members of the group. It is suggested that more than one mechanism, including intervention by the mother and by close female relatives,may be important in rank acquisition among peers.     

Prostaglandin E1 binding and adenylate cyclase activation in normal and transformed fibroblasts

The binding of [3H]prostaglandin E1 to membranes of clones of normal rat kidney fibroblasts (NRK cells) has been measured. Cell lines that responded to prostaglandin E1, such as NRK and NRK transformed with Schmitt-Ruppin strain of Rous sarcoma virus (SR-NRK cells), have a high affinity prostaglandin E1 binding site. Murine-sarcoma-virus-transformed lines of NRK cells are unresponsive to prostaglandin E1 and have reduced prostaglandin E1 binding Exposure of cells to prostaglandin E1 results both in decreased prostaglandin E1 responsiveness and reduced prostaglandin E1 binding. Activation of adenylate cyclase is correlated to binding of prostaglandin E1 to receptors in both NRK and SR-NRK cell membranes. Mathematical models suggest that GTP decreases the affinity of hormone for its receptor while increasing the catalytic efficiency of adenylate cyclase, and that aggregates of occupied receptors may play an important role in the activation of adenylate cyclase.     

Antagonism of benzodiazepine binding in rat and human brain by Antilirium.

Physostigmine (Antilirium^R) has been reported to reverse benzodiazepine- induced sleep or coma in man and prevent death in animals. Accordingly, we investigated the effect of Antilirium upon benzodiazepine binding to both rat and human brain. We report that Antilirium inhibits ³H-diazepam and ³H-flunitrazepam binding in a dose-dependent manner. The degree of inhibition of binding by Antilirium correlates with the affinity of benzodiazepine for its “receptor” such that diazepam is more affected than flunitrazepam. The inhibition is rapid but the kinetics are complex with only doses of Antilirium showing competitive inhibition when studied at equilibrium. These results may explain, at least in part, the effectiveness of Antilirium at reversing benzodiazepine-induced hypnosis without necessarily implicating a cholinergic mechanism.     

Light-induced changes of cyclic GMP content in frog retinal rod outer segments measured with rapid freezing and microdissection

Cyclic GMP concentration was measured in the rod outer segments (ROS) of the isolated frog retinas. Retinas were quickly frozen in 0.5 s after the short light flash producing 90%-saturated late receptor potential (2,000 rhodopsins bleached per rod). ROS were obtained by microdissection, and cGMP levels were determined by radioimmunoassay method. No detectable changes in cGMP concentration was found in this stimulus condition. Dark-adapted ROS contained 46.3 ± 1.5 pmole cGMP per mg dry weight, flash-illuminated ones –45 ± 2 pmole/mg. 3-s bright illumination (ca. 10⁷ rhodopsins bleached per rod per second) led to approximately 30% drop in cGMP content. It is supposed that the main part of cGMP within the ROS is in the bound state and therefore fast light-induced changes in its minor free fraction may escape the detection.