Bioorthogonal chemistry: applications in activity-based protein profiling

The close interaction between organic chemistry and biology goes back to the late 18th century, when the modern natural sciences began to take shape. After synthetic organic chemistry arose as a discipline, organic chemists almost immediately began to pursue the synthesis of naturally occurring compounds, thereby contributing to the understanding of their functions in biological processes. Research in those days was often remarkably interdisciplinary; in fact, it constituted chemical biology research before the phrase even existed. For example, histological dyes, both of an organic and inorganic nature, were developed and applied by independent researchers (Gram and Golgi) with the aim of visualizing cellular substructures (the bacterial cell wall and the Golgi apparatus). Over the years, as knowledge within the various fields of the natural sciences deepened, research disciplines drifted apart, becoming rather monodisciplinary. In these years, broadly ranging from the end of World War II to about the 1980s, organic chemistry continued to impact life sciences research, but contributions were of a more indirect nature. As an example, the development of the polymerase chain reaction, from which molecular biology and genetics research have greatly profited, was partly predicated on the availability of synthetic oligonucleotides. These molecules first became available in the late 1960s, the result of organic chemists pursuing the synthesis of DNA oligomers primarily because of the synthetic challenges involved. Today, academic natural sciences research is again becoming more interdisciplinary, and sometimes even multidisciplinary. What was termed "chemical biology" by Stuart Schreiber at the end of the last century can be roughly described as the use of intellectually chemical approaches to shed light on processes that are fundamentally rooted in biology. Chemical tools and techniques that are developed for biological studies in the exciting and rapidly evolving field of chemical biology research include contributions from many areas of the multifaceted discipline of chemistry, and particularly from organic chemistry. Researchers apply knowledge inherent to organic chemistry, such as reactivity and selectivity, to the manipulation of specific biomolecules in biological samples (cell extracts, living cells, and sometimes even animal models) to gain insight into the biological phenomena in which these molecules participate. In this Account, we highlight some of the recent developments in chemical biology research driven by organic chemistry, with a focus on bioorthogonal chemistry in relation to activity-based protein profiling. The rigorous demands of bioorthogonality have not yet been realized in a truly bioorthogonal reagent pair, but remarkable progress has afforded a range of tangible contributions to chemical biology research. Activity-based protein profiling, which aims to obtain information on the workings of a protein (or protein family) within the larger context of the full biological system, has in particular benefited from these advances. Both activity-based protein profiling and bioorthogonal chemistry have been around for approximately 15 years, and about 8 years ago the two fields very profitably intersected. We expect that each discipline, both separately and in concert, will continue to make important contributions to chemical biology research.     

Optical properties of apple skin and flesh in the wavelength range from 350 to 2200 nm

Optical measurement of fruit quality is challenging due to the presence of a skin around the fruit flesh and the multiple scattering by the structured tissues. To gain insight in the light-tissue interaction, the optical properties of apple skin and flesh tissue are estimated in the 350-2200 nm range for three cultivars. For this purpose, single integrating sphere measurements are combined with inverse adding-doubling. The observed absorption coefficient spectra are dominated by water in the near infrared and by pigments and chlorophyll in the visible region, whose concentrations are much higher in skin tissue. The scattering coefficient spectra show the monotonic decrease with increasing wavelength typical for biological tissues with skin tissue being approximately three times more scattering than flesh tissue. Comparison to the values from time-resolved spectroscopy reported in literature showed comparable profiles for the optical properties, but overestimation of the absorption coefficient values, due to light losses.     

Cloning, characterization and functionality of the orotidine-5'-phosphate decarboxylase gene (URA3) of the glycolipid-producing yeast Candida bombicola

Candida bombicola is a yeast species known to synthesize glycolipids. Although these glycolipids find several industrial, cosmetic and pharmaceutical applications, very little is known about the genetics of C. bombicola. A basic tool for genetic study and modification is the availability of an efficient transformation and selection system. In order to develop such a system, the URA3 gene of Candida bombicola was isolated using degenerate PCR and genomic walking. The gene encodes for an enzyme of 262 amino acids and shows high homology with the known orotidine-5'-phosphate decarboxylases of several other yeast species. The functionality of the gene was proved by complementation of a URA3-negative Saccharomyces cerevisiae strain.     

Real‐time density‐based crowd simulation

Virtual characters in games and simulations often need to plan visually convincing paths through a crowded environment. This paper describes how crowd density information can be used to guide a large number of characters through a crowded environment. Crowd density information helps characters avoid congested routes that could lead to traffic jams. It also encourages characters to use a wide variety of routes to reach their destination. Our technique measures the desirability of a route by combining distance information with crowd density information. We start by building a navigation mesh for the walkable regions in a polygonal two‐dimensional (2‐D) or multilayered three‐dimensional (3‐D) environment. The skeleton of this navigation mesh is the medial axis. Each walkable region in the navigation mesh maintains an up‐to‐date density value. This density value is equal to the area occupied by all the characters inside a given region divided by the total area of this region. These density values are mapped onto the medial axis to form a weighted graph. An A^* search on this graph yields a backbone path for each character, and forces are used to guide the characters through the weighted environment. The characters periodically replan their routes as the density values are updated. Our experiments show that we can compute congestion‐avoiding paths for tens of thousands of characters in real‐time. Copyright © 2012 John Wiley & Sons, Ltd.     

Carbonation of steel slag for CO2 sequestration: leaching of products and reaction mechanisms

Carbonation of industrial alkaline residues can be used as a CO2 sequestration technology to reduce carbon dioxide emissions. In this study, steel slag samples were carbonated to a varying extent. Leaching experiments and geochemical modeling were used to identify solubility-controlling processes of major and trace elements, both with regard to carbonation mechanisms and the environmental properties of the (carbonated) steel slag. Carbonation was shown to reduce the leaching of alkaline earth metals (except Mg) by conversion of Ca-phases, such as portlandite, ettringite, and Ca-(Fe)-silicates into calcite, possibly containing traces of Ba and Sr. The leaching of vanadium increased substantially upon carbonation, probably due to the dissolution of a Ca-vanadate. The reactive surface area of Al- and Fe-(hydr)oxides increased with the carbonation degree, which tends to reduce the leaching of sorption-controlled trace elements. Sorption on Mn- (hydr)oxides was found to be required to adequately model the leaching of divalent cations, but was not influenced by carbonation. Consideration of these three distinct reactive surfaces and possible (surface) precipitation reactions resulted in adequate modeling predictions of oxyanion and trace metal leaching from (carbonated) steel slag. Hence, these surfaces exert a major influence on the environmental properties of both fresh and carbonated steel slag.     

Make No Big Plans

In the face of ‘derivative architecture’, artificial commercial speculation that was a feature of the previous economic boom, Michelle Provoost and Wouter Vanstiphout of Crimson Architectural Historians call for a new understanding of the real city and its actual needs, basing interventions on observations rooted in society and spatial structures.