Directed evolution of mammalian cytochrome P450 enzymes involved in xenobiotic metabolism

Directed evolution of cytochrome P450 enzymes represents an attractive means of generating novel catalysts for specialized applications. Xenobiotic-metabolizing P450s are particularly well suited to this approach due to their inherent wide substrate specificity. In the present study, a novel method for DNA shuffling was developed using an initial restriction enzyme digestion step, followed by elimination of long parental sequences by size-selective filtration. P450 2C forms were subjected to a single round of shuffling then coexpressed with reductase in E. coli. A sample (54 clones) of the resultant library was assessed for sequence diversity, hemo- and apoprotein expression, and activity towards the substrate indole. All mutants showed a different RFLP pattern compared to all parents, suggesting that the library was free from contamination by parental forms. Haemoprotein expression was detectable in 45/54 (83%) of the mutants sampled. Indigo production was less than or comparable to the activities of one or more of the parental P450s, but three mutants showed indirubin production in excess of that seen with any parental form, representing a gain of function. In conclusion, a method is presented for the effective shuffling of P450 sequences to generate diverse libraries of mutant P450s containing a high proportion of correctly folded hemoprotein, and minimal contamination with parental forms.

Site-directed mutagenesis of dimethylsulfoxide reductase from Rhodobacter capsulatus: The critical roles of tyrosine-114 and tryptophan-116

The crystal structure of six functionally-distinct enzymes of the DMSO reductase family of molybdenum enzymes has revealed that the tertiary structure of the polypeptide that binds the bis(MGD)Mo cofactor is highly conserved. Differences in the catalytic properties of enzymes of this family are almost certainly dependent upon differences in the structure ofthe MO active site. In DMSO reductase from Rhodobacter species tryptophan- 116 (W 116) hydrogen-bonds to an 0x0 group coordinated to the MO ion. In addition a second amino acid side chain from tyrosine-114 (Y 114) is in close proximity to the 0x0 group. We have investigated the role of Y 114 and W 116 in DMSO reductase using site-directed mutagenesis,

A Practical Teaching Course in Directed Protein Evolution Using the Green Fluorescent Protein as a Model

Protein engineering is a powerful tool, which correlates protein structure with specific functions, both in applied biotechnology and in basic research. Here, we present a practical teaching course for engineering the green fluorescent protein (GFP) from Aequorea victoria by a random mutagenesis strategy using error-prone polymerase chain reaction. Screening of bacterial colonies transformed with random mutant libraries identified GFP variants with increased fluorescence yields. Mapping the three-dimensional structure of these mutants demonstrated how alterations in structural features such as the environment around the fluorophore and properties of the protein surface can influence functional properties such as the intensity of fluorescence and protein solubility.

Snakes and kittens in the grass: No evidence for preferential processing of fear-relevant animals in visual search

Ohman and colleagues provided evidence for preferential processing of pictures depicting fear-relevant animals by showing that pictures of snakes and spiders are found faster among pictures of fiowers and mushrooms than vice versa and that the speed of detecting fear-relevant animals was not affected by set size whereas the speed of detecting fiowers/mushrooms was. Experiment 1 replicated this finding. Experiment 2, however, found similar search advantages when pictures of cats and horses or of wolves and big cats were to be found among pictures of flowers and mushrooms. Moreover, Experiment 3, in a within subject comparison, failed to find faster identification of snakes and spiders than of cats and horses among flowers and mushrooms. The present findings seem to indicate that previous reports of preferential processing of pictures of snakes and spiders in a visual search task may reflect a processing advantage for animal pictures in general rather than fear-relevance.

QUADRANT-SEARCHING: A NEW TECHNIQUE TO REDUCE THE SEARCH SPACE OF THE INVERSE PROBLEM OF EIT USING BEM TO THE DIRECT PROBLEM

The image reconstruction using the EIT (Electrical Impedance Tomography) technique is a nonlinear and ill-posed inverse problem which demands a powerful direct or iterative method. A typical approach for solving the problem is to minimize an error functional using an iterative method. In this case, an initial solution close enough to the global minimum is mandatory to ensure the convergence to the correct minimum in an appropriate time interval. The aim of this paper is to present a new, simple and low cost technique (quadrant-searching) to reduce the search space and consequently to obtain an initial solution of the inverse problem of EIT. This technique calculates the error functional for four different contrast distributions placing a large prospective inclusion in the four quadrants of the domain. Comparing the four values of the error functional it is possible to get conclusions about the internal electric contrast. For this purpose, initially we performed tests to assess the accuracy of the BEM (Boundary Element Method) when applied to the direct problem of the EIT and to verify the behavior of error functional surface in the search space. Finally, numerical tests have been performed to verify the new technique.

Characterization of rat behavior in the elevated plus-maze using a directed graph

The elevated plus-maze is a device widely used to assess rodent anxiety under the effect of several treatments, including pharmacological agents. The animal is placed at the center of the apparatus, which consists of two open arms and two arms enclosed by walls, and the number of entries and duration of stay in each arm are measured for a 5-min exposure period. The effect of an anxiolytic drug is to increase the percentage of time spent and number of entries into the open arms. In this work, we propose a new measure of anxiety levels in the rat submitted to the elevated plus-maze. We represented the spatial structure of the elevated plus-maze in terms of a directed graph and studied the statistics of the rat`s transitions between the nodes of the graph. By counting the number of times each transition is made and ordering them in descending frequency we represented the rat`s behavior in a rank-frequency plot. Our results suggest that the curves obtained under different pharmacological conditions can be well fitted by a power law with an exponent sensitive to both the drug type and the dose used. (C) 2009 Elsevier B.V. All rights reserved.

Charles Wilkes, a US Exploring Expedition and the US` search for its place in the world (1838-1842)

The main focus of this essay is the first American round-the-world scientific voyage, the U. S Exploring Expedition, which took place between 1838 and 1841 and was lead by Lieutenant Charles Wilkes. Here, I discuss the purposes of this expedition in the context of the voyages of circumnavigation accomplished by the various European powers during the same period.

Search for Chronic Beryllium Disease Among Sarcoidosis Patients in Ontario, Canada

Chronic beryllium disease (CBD) is clinically similar to other granulomatous diseases such as sarcoidosis. It is often misdiagnosed if a thorough occupational history is not taken. When appropriate, a beryllium lymphocyte proliferation tests (BeLPT) need to be performed. We aimed to search for CBD among currently diagnosed pulmonary sarcoidosis patients and to identify the occupations and exposures in Ontario leading to CBD. Questionnaire items included work history and details of possible exposure to beryllium. Participants who provided a history of previous work with metals underwent BeLPTs and an ELISPOT on the basis of having a higher pretest probability of CBD. Among 121 sarcoid patients enrolled, 87 (72%) reported no known previous metal dust or fume exposure, while 34 (28%) had metal exposure, including 17 (14%) with beryllium exposure at work or home. However, none of these 34 who underwent testing had positive test results. Self-reported exposure to beryllium or metals was relatively common in these patients with clinical sarcoidosis, but CBD was not confirmed using blood assays in this population.

2-perfect directed m-cycle systems can be equationally defined for m=3,4, and 5 only

It is shown that quasigroups constructed using the standard construction from 2-perfect directed m-cycle systems are precisely the finite members of a variety if and only if m=3, 4 or 5.

Self-Directed Behavioral Family Intervention for Parents of Oppositional Children in Rural and Remote Areas

Twenty-four parents of oppositional preschoolers were randomly assigned to either a self-directed behavioral family intervention condition (SD) or to a waitlist control group (WL). The self-directed parent training program based on self-regulation principles, consisted of a written information package and weekly telephone consultations for 10 weeks. At posttest, in comparison to the WL group, children in the SD group had lower levels of behavior problems on parent report measures of child behavior. At posttreatment, parents in the SD condition reported increased levels of parenting competence and lower levels of dysfunctional parenting practices as compared to parents in the WL condition. In addition, mothers reported lower levels of anxiety, depression, and stress as compared to mothers in the WL condition at posttreatment. Using mother's reports, gains in child behavior and parenting practices achieved at posttreatment were maintained at 4-month follow-up.

Outbreak of vancomycin-resistant enterococci in a tertiary hospital: The lack of effect of measures directed mainly by surveillance cultures and differences in response between Enterococcus faecium and Enterococcus faecalis

To describe the effect of active surveillance to control vancomycin-resistant enterococci (VRE) after an outbreak, 549 surveillance rectal cultures were performed in 308 patients (35% positive). An educational intervention to prevent transmission was implemented. Infection and colonization by VR-Enterococcus faecalis decreased, but Enterococcus faecium persisted despite control measures. Infections by VR-E faecalis fell to zero in 2008. We observed difficulties in controlling colonization with measures directed mainly by surveillance cultures and differences between responses of E faecium and E faecalis.