Standard Graphics Software Research Articles

BracketMaker: Visualization and optimization of chemical protein synthesis.

Chemical protein synthesis (CPS), in which custom peptide segments of ~20-60 aa are produced by solid-phase peptide synthesis and then stitched together through sequential ligation reactions, is an increasingly popular technique. The workflow of CPS is often depicted with a "bracket" style diagram detailing the starting segments and the order of all ligation, desulfurization, and/or deprotection steps to obtain the product protein. Brackets are invaluable tools for comparing multiple possible synthetic approaches and serve as blueprints throughout a synthesis. Drawing CPS brackets by hand or in standard graphics software, however, is a painstaking and error-prone process. Furthermore, the CPS field lacks a standard bracket format, making side-by-side comparisons difficult. To address these problems, we developed BracketMaker, an open-source Python program with built-in graphic user interface (GUI) for the rapid creation and analysis of CPS brackets. BracketMaker contains a custom graphics engine which converts a text string (a protein sequence annotated with reaction steps, introduced herein as a standardized format for brackets) into a high-quality vector or PNG image. To aid with new syntheses, BracketMaker's "AutoBracket" tool automatically performs retrosynthetic analysis on a set of segments to draft and rank all possible ligation orders using standard native chemical ligation, protection, and desulfurization techniques. AutoBracket, in conjunction with an improved version of our previously reported Automated Ligator (Aligator) program, provides a pipeline to rapidly develop synthesis plans for a given protein sequence. We demonstrate the application of both programs to develop a blueprint for 65 proteins of the minimal Escherichia coli ribosome.

Three dimensional reconstruction of two-cell mouse embryo by laser scanning microscopy

The direct method of volumetric parameters’ measurement of early mammal embryo was developed. The sample preparation was based on embryo cryofixation followed by laser scanning microscopy. Digital image processing and three dimensional reconstruction of embryos was performed with standard graphic software. The availability of a developed technique for the analysis of cell physiology at cultivation conditions was demonstrated on isolated two-cell mouse embryo.

Data coding tools for color-coded vector nanolithography

We propose and demonstrate the ability and efficiency of using a universal file format for a nanolithography pattern. A problem faced by the physicists working in the field of nanolithography is a lack of a flexible pattern design software (possibly open–source) that could be applied in combination with a broad range of commercial scanning probe microscope (SPM) systems. The current nanolithography software packages are device–specific and not portable. Therefore, it is impossible to make a lithography pattern and share it with fellow physicists working on a networked sub-system. In this paper we describe the software designed to read and interpret a nanolithography pattern stored in a Windows Metafile (WMF) standard graphic format and next to draw it on a substrate using an SPM tip. The nanolithography parameters like height, velocity, feedback force, etc. are coded in the color of the WMF onto the RGB channels of the image establishing a distinct relation between a graphical feature (color) and the used nanolithography scheme (voltage, height, etc.). The concept enables preparation of complex patterns using any standard graphic software and aids an intuitive recognition of the mode and parameters set for a pattern. The advantages of using a WMF over other approaches and the universal scope of the software are discussed.

Cultured rat trachea as a model for the study of ciliary abundance: the effect of oxygen.

Cultured rat trachea as a model for the study of ciliary abundance: the effect of oxygen.

Quantification of immunological membrane reactions employing a digital desk top scanner and standard graphics software

Many common techniques used in biochemical and molecular biology analysis involve the generation of signals by immunological or hybridization detection reactions on membranes or photographic films (e.g. ‘windrose blots’, immunoblots). The possibility to undertake comparative and quantitative evaluation of these signals is a basic requirement in most applications. However, visual inspection of immunological detection by colour reactions or by autoradiography using a photographic film does not usually provide a reliable basis for the quantification and interpretation of results. Thus, there is a need for a reproducible, (semi-)quantitative method with an option for numeric read-out and comparable graphic display. Here, we describe a simple method for the reliable and reproducible evaluation of signals generated on membranes or photographic films which combines standard graphics software with a low-budget desk top scanner.

Graphical analysis and visualization of 3-D properties of molecules and solids

A simple approach is presented for visualizing three-dimensional properties of molecular and crystalline systems by using PC-based molecular drawing software. This allows a scientist with lower-cost PC-graphics capability to carry out analysis of data, such as wave functions and electron density, which would otherwise require a dedicated graphics workstation and expensive specialized software. In this approach, a data set [x,y,z,f1(x,y,z)] is transformed to a new set of data [x,y,z] for values of f1 meeting specified requirements. The function f1, which varies throughout a chemical system is difficult to visualize. However, a more manageable data set is obtained if the set of Cartesian coordinates corresponding to locations in the system where f1 has a specified value are used. This set of points can then be visualized and plotted with standard graphics software or PC-based molecular modeling programs. In addition, the use of PC-based molecular graphics permits one to superimpose the data describing molecular properties on drawings of the molecular geometry. The entire object can then be rotated to facilitate a clear analysis of the property of the molecule.

Conveying Principles of Finite Strain with Standard Graphics Software

Finite-strain concepts can be effectively illustrated using widely available computer graphics software. Many programs have the ability to “deform” objects, making it possible for students to study the effects of strain on passive markers which they have created.