Block Model (block + model)

Distribution by Scientific Domains

Selected Abstracts


EVOLUTION, Issue 6 2006
H. Allen Orr
Abstract Several recent theoretical studies of the genetics of adaptation have focused on the mutational landscape model, which considers evolution on rugged fitness landscapes (i.e., ones having many local optima). Adaptation in this model is characterized by several simple results. Here I ask whether these results also hold on correlated fitness landscapes, which are smoother than those considered in the mutational landscape model. In particular, I study the genetics of adaptation in the block model, a tunably rugged model of fitness landscapes. Considering the scenario in which adaptation begins from a high fitness wild-type DNA sequence, I use extreme value theory and computer simulations to study both single adaptive steps and entire adaptive walks. I show that all previous results characterizing single steps in adaptation in the mutational landscape model hold at least approximately on correlated landscapes in the block model; many entire-walk results, however, do not. [source]

Octenidine in root canal and dentine disinfection ex vivo

L. Tandjung
Abstract Aim, The aim of the present study was to investigate the antimicrobial activity of octenidine on Enterococcus faecalis ATCC 29212 in a dentine block model. Methodology, Fifty-six root segments of extracted human teeth were infected with E. faecalis for 4 weeks. Octenidine-phenoxyethanol gel (1 : 1) was applied for different timing: 1 min, 10 min, 7 days and in a different formula (1 : 3) for 10 min. Three samples were chosen for the group with placebo gel and for the group without infection (negative control). Dentine samples were collected, and the total count of bacteria and colony-forming units were determined. In addition, for controls and the 10 min group with 1 : 1 gel, the proportion of viable bacteria (PVB) was assessed. Results, Octenidine was particularly effective after incubation periods of 10 min and 7 days. The mean PVB decreased significantly from 57.2% to 5.7% after 10 min application. After 7 days, only one of 10 samples showed positive culture. Conclusion, The present study showed the effectiveness of octenidine against E. faecalis in dentine disinfection. Further laboratory and clinical studies are required. [source]

Octanol Modulation of Neuronal Nicotinic Acetylcholine Receptor Single Channels

ALCOHOLISM, Issue 11 2004
Yi Zuo
Background: We have previously shown that alcohols exert a dual action on neuronal nicotinic acetylcholine receptors (AChRs), with short-chain alcohols potentiating and long-chain alcohols inhibiting acetylcholine (ACh)-induced whole-cell currents. At the single-channel level, ethanol increased the channel open probability and prolonged the channel open time and burst duration. In this study, we examined the detailed mechanism of the inhibitory action of the long-chain alcohol n -octanol on the neuronal nicotinic AChR. Methods: Single-channel currents induced by application of 30 nm ACh were recorded with the patch-clamp technique from human embryonic kidney cells stably expressing the human ,4,2 AChR. Results: Several single-channel parameters were markedly changed by octanol. At least two conductance-state currents were induced by low concentrations of ACh, and octanol increased the proportion of the low-conductance-state current relative to the high-conductance-state current without changing the current amplitude. Major analyses of temporal properties of single-channel currents were performed on the high-conductance-state currents. Octanol decreased the burst duration and duration of openings within burst and prolonged the mean closed time. All of these changes contributed to the decrease in the open probability in a concentration-dependent manner. Conclusions: Several aspects of octanol action on neuronal AChRs at the single-channel level are compatible with an atypical open channel block model reported with muscle nicotinic AChRs. The potentiating action of short-chain alcohols and the inhibitory action of long-chain alcohols on the neuronal nicotinic AChR are mediated through different mechanisms. [source]

In silico protein design by combinatorial assembly of protein building blocks

PROTEIN SCIENCE, Issue 10 2004
Hui-Hsu (Gavin) Tsai
Abstract Utilizing concepts of protein building blocks, we propose a de novo computational algorithm that is similar to combinatorial shuffling experiments. Our goal is to engineer new naturally occurring folds with low homology to existing proteins. A selected protein is first partitioned into its building blocks based on their compactness, degree of isolation from the rest of the structure, and hydrophobicity. Next, the protein building blocks are substituted by fragments taken from other proteins with overall low sequence identity, but with a similar hydrophobic/hydrophilic pattern and a high structural similarity. These criteria ensure that the designed protein has a similar fold, low sequence identity, and a good hydrophobic core compared with its native counterpart. Here, we have selected two proteins for engineering, protein G B1 domain and ubiquitin. The two engineered proteins share ,20% and ,25% amino acid sequence identities with their native counterparts, respectively. The stabilities of the engineered proteins are tested by explicit water molecular dynamics simulations. The algorithm implements a strategy of designing a protein using relatively stable fragments, with a high population time. Here, we have selected the fragments by searching for local minima along the polypeptide chain using the protein building block model. Such an approach provides a new method for engineering new proteins with similar folds and low homology. [source]