A role for Edman degradation in proteome studies

Advances in protein database design and the software used to access the sequence data has led to progress in using protein attributes such as amino acid composition and peptide masses to identify proteins separated by two-dimensional electrophoresis. However, Edman degradation remains the principal technique for protein identification and it presents a significant bottleneck in the progress towards rapid protein identification. Simple modifications to the sequencing hardware, which automate the delivery of protein spots into the sequencer, and parallel sequencing of the protein spots represent a significant advance in the use of Edman degradation to rapidly generate the powerful protein attribute, an N-terminal sequence tag.     

How far is it to the nearest hospital? Calculating distances using the Statistics Canada Postal Code Conversion File

This report demonstrates how to calculate distances between points described in terms of latitude and longitude, using the Postal Code Conversion File (PCCF) and other files available from the Geography Division of Statistics Canada. Examples based on hospital data show how the results can be summarized in the form of tables, figures, or maps. Aerial distance to the nearest hospital is a crude but objective indicator of geographic accessibility to hospital services. Distances were calculated between enumeration area centroids for the population and blockface or enumeration area centroids for the hospitals. The median aerial distance to the nearest hospital facility in Canada was less than 3 km, while the mean distance was about 6 km. For teaching hospitals, the median aerial distance was a little less than 30 km, while the mean distance was a little more than 90 km. As most health files for administrative and research purposes contain postal codes, these techniques have potentially wide application.     

Casual reasoning in planning1

Reasoning about actions necessarily involves tracking the truth of assertions about the world over time. The SIPE planning system retains the efficiency of the STRIPS assumption for this while enhancing expressive power by allowing the specification of a causl theory. Separation of knowledge about causality from knowledge about actions relieves operators of much of their representational burden and allows them to be applicable in a wide range of contexts. The implementation of causal theories is described, together with examples and evaluations of the system's expressive power and efficiency.     

Development of the gel pond technology

A review of the development of the gel pond technology is presented. First, the emergence and growth of solar pond technology since the 1950's is described. The inherent problems encountered with the conventional salt gradient ponds are discussed, leading to the concept of the solar gel pond in which the salt gradient layer in the former is replaced by a transparent polymer gel. The major work in the first phase dealt with the experimental development of a polymer gel which met certain selection criteria. The criteria considered included transmissivity, stability of physical and chemical properties, high viscosity and other physical and optical properties. The gradual development of the polymer gel through an alternating process of testing and elimination and evaluation of relevant properties of the gel has been described. Modeling and optimization studies of the solar gel pond have been presented. Bansal and Kaushik's model for a salt gradient pond has been modified for a solar gel pond, and the results of the simulation are presented in a graphical form to serve as a quick reference for estimation of pond surface area, depth and flow rate for heat extraction depending on the extreme temperature required in the storage zone and the required heat load. Then, a cost-benefit economic analysis compares the economics of a solar gel pond with a conventional salt gradient pond. The construction of an experimental gel pond (18 m²) at The University of New Mexico is described, and the results of the study are summarized. Information on commercial scale ponds at Chamberino, New Mexico (110 m²), and in Albuquerque, New Mexico (400 m²), is provided. The review of the technology demonstrates the immense potential of the gel pond as a source of alternate energy for the years ahead.     

Annexin 1 Is a Component of eATP-Induced Cytosolic Calcium Elevation in Arabidopsis thaliana Roots

Extracellular ATP (eATP) has long been established in animals as an important signalling molecule but this is less understood in plants. The identification of Arabidopsis thaliana DORN1 (Does Not Respond to Nucleotides) as the first plant eATP receptor has shown that it is fundamental to the elevation of cytosolic free Ca²⁺ ([Ca²⁺]_cyt) as a possible second messenger. eATP causes other downstream responses such as increase in reactive oxygen species (ROS) and nitric oxide, plus changes in gene expression. The plasma membrane Ca²⁺ influx channels involved in eATP-induced [Ca²⁺]_cyt increase remain unknown at the genetic level. Arabidopsis thaliana Annexin 1 has been found to mediate ROS-activated Ca²⁺ influx in root epidermis, consistent with its operating as a transport pathway. In this study, the loss of function Annexin 1 mutant was found to have impaired [Ca²⁺]_cyt elevation in roots in response to eATP or eADP. Additionally, this annexin was implicated in modulating eATP-induced intracellular ROS accumulation in roots as well as expression of eATP-responsive genes.     

Geomorphic comparison of two Atlantic coastal rivers: Toward an understanding of physical controls on Atlantic salmon habitat

River channel substrate size and mobility are important to Atlantic salmon spawning and rearing success. We compare morphology and bed sediment between two North American Atlantic coastal streams (Narraguagus River, Maine, USA and Jacquet River, New Brunswick, Canada). The watersheds have similar drainage areas and mean annual precipitation, but differing relief structure, channel longitudinal profiles and numbers of returning salmon. The lower‐relief Narraguagus River is segmented into steeper (gradient >0.002) and flatter reaches (gradient <0.0005). Flat reaches, including mainstem lakes, act as sediment sinks, preventing the continuity of downstream sediment transport. Based on field measurements, the Narraguagus River has a larger high‐flow width to depth ratio than the Jacquet River, but this difference is principally the result of outliers from low‐gradient channel reaches. Measurements of substrate grain size reveal finer river‐bed sediments on the Narraguagus River, however, Shields parameter calculations indicate that bed sediment should be mobile during high flows in both streams. We use the Shields equation to predict grain size based on channel slope, width and drainage area measured from digital elevation models (DEM) and aerial photographs. Predictions of median grain size agree with field measurements within a factor of 2 for 62–70% of the survey stations. We suggest ways that model misfits may provide opportunities to prioritize reach‐based restoration efforts. Based on expected grain size, we estimate 62% spawning and 68% rearing habitat along the length of the Narraguagus River, and 28 and 95% respectively on the Jacquet. Overall, glacial history and relief structure appear to be the first‐order controls on substrate grain size and habitat quality in these two rivers. Copyright © 2010 John Wiley & Sons, Ltd.     

'98 Escherichia coli SWISS-2DPAGE database update

The combination of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), computer image analysis and several protein identification techniques allowed the Escherichia coli SWISS-2DPAGE database to be established. This is part of the ExPASy molecular biology server accessible through the WWW at the URL address http://www.expasy.ch/ch2d/ch2d-top.html . Here we report recent progress in the development of the E. coli SWISS-2DPAGE database. Proteins were separated with immobilized pH gradients in the first dimension and sodium dodecyl sulfate-polyacrylamide gel electrophoresis in the second dimension. To increase the resolution of the separation and thus the number of identified proteins, a variety of wide and narrow range immobilized pH gradients were used in the first dimension. Micropreparative gels were electroblotted onto polyvinylidene difluoride membranes and spots were visualized by amido black staining. Protein identification techniques such as amino acid composition analysis, gel comparison and microsequencing were used, as well as a recently described Edman "sequence tag" approach. Some of the above identification techniques were coupled with database searching tools. Currently 231 polypeptides are identified on the E. coli SWISS-2DPAGE map: 64 have been identified by N-terminal microsequencing, 39 by amino acid composition, and 82 by sequence tag. Of 153 proteins putatively identified by gel comparison, 65 have been confirmed. Many proteins have been identified using more than one technique. Faster progress in the E. coli proteome project will now be possible with advances in biochemical methodology and with the completion of the entire E. coli genome.