Search

Current methods for single-molecule orientation localization microscopy (SMOLM) require optical setups and algorithms that can be prohibitively slow and complex, limiting widespread adoption for biological applications. We present POLCAM, a simplified SMOLM method based on polarized detection using a polarization camera, which can be easily implemented on any wide-field fluorescence microscope. To make polarization cameras compatible with single-molecule detection, we developed theory to minimize field-of-view errors, used simulations to optimize experimental design and developed a fast algorithm based on Stokes parameter estimation that can operate over 1,000-fold faster than the state of the art, enabling near-instant determination of molecular anisotropy. To aid in the adoption of POLCAM, we developed open-source image analysis software and a website detailing hardware installation and software use. To illustrate the potential of POLCAM in the life sciences, we applied our method to study α-synuclein fibrils, the actin cytoskeleton of mammalian cells, fibroblast-like cells and the plasma membrane of live human T cells., (© 2024. The Author(s).)

Unlabelled: Taverna is an application that eases the integration of tools and databases for life science research by the construction of workflows. The Taverna Interaction Service extends the functionality of Taverna by defining human interaction within a workflow and acting as a mediation layer between the automated workflow engine and one or more users., Availability: Taverna, the Interaction Service plug-in and web application are available as open source and can be downloaded from http://taverna.sourceforge.net/

Unlabelled: OneChannelGUI is an add-on Bioconductor package providing a new set of functions extending the capability of the affylmGUI package. This library provides a graphical interface (GUI) for Bioconductor libraries to be used for quality control, normalization, filtering, statistical validation and data mining for single channel microarrays. Affymetrix 3' expression (IVT) arrays as well as the new whole transcript expression arrays, i.e. gene/exon 1.0 ST, are actually implemented. oneChannelGUI is available for most platforms on which R runs, i.e. Windows and Unix-like machines., Availability: http://www.bioconductor.org/packages/2.0/bioc/html/oneChannelGUI.html

In the light of the increasing number of biological databases, their integration is a fundamental prerequisite for answering complex biological questions. Database integration, therefore, is an important area of research in bioinformatics. Since most of the publicly available life science databases are still exclusively exchanged by means of proprietary flat files, database integration requires parsers for very different flat file formats. Unfortunately, the development and maintenance of database specific flat file parsers is a nontrivial and time-consuming task, which takes considerable effort in large-scale integration scenarios. This paper introduces heuristically based concepts for automatic structure extraction from life science database flat files. On the basis of these concepts the FlatEx prototype is developed for the automatic conversion of flat files into XML representations.

The aim of the present study is to emphasize the applicability and versatility of the allometric equation in the biological sciences. This equation (Y = a x Mb) was introduced by Huxley (1932) for intra- and interspecific comparisons of morphological, physiological and ecological variables (Y), when they are expressed as functions of body mass (M). The regression analysis of the experimental data, plotted in a double logarithmic scale, yields a straight line, which is equivalent to the logarithmic form of the above mentioned allometric equation [log Y = log(a) + (b) x log(M)]. Only the exponent (b) can be calculated a priori for a given function, based firstly on the corresponding dimensional analysis in accordance with the MLT-system of physics, and secondly on one of the theories of biological similarity, while parameter (a) is of empirical nature. A relevant feature of the allometric equations is that they can be treated algebraically to obtain allometric ratios, mass independent numbers (MIN), and even dimensionless numbers (M0L0T0), which are valid for all organisms pertaining to the same taxonomic classification.