Chaotic mixing using source�Csink microfluidic flows in a PDMS chip

We present an active fixed-volume mixer based on the creation of multiple source–sink microfluidic flows in a polydimethylsiloxane (PDMS) chip without the need of external or internal pumps. To do so, four different pressure-controlled actuation chambers are arranged on top of the 5 μl volume of the mixing chamber. After the mixing volume is sealed/fixed by microfluidic valves made using ‘microplumbing technology’, a virtual source–sink pair is created by pressurizing one of the membranes and, at the same time, releasing the pressure of a neighboring one. The pressurized air deforms the thin membrane between the mixing and control chambers and creates microfluidic flows from the squeezed region (source) to the released region (sink) where the PDMS membrane is turned into the initial state. Several schemes of operation of virtual source–sink pairs are studied. In the optimized protocol, mixing is realized in just a sub-second time interval, thanks to the implementation of chaotic advection.     

Improvement of hepatocyte-specific gene expression by a targeted colchicine prodrug

Colchicine, an established tubulin inhibitor, interferes with the trafficking of endocytotic vesicles and thereby promotes the escape of lysosome-entrapped compounds. To improve its potency and cell specificity, a targeted prodrug of colchicine was synthesized by conjugation to a high-affinity ligand (di-N(alpha),N(epsilon)-(5-(2-acetamido-2-deoxy-beta-D-galactopyranosyloxy)pentanomido)lysine, K(GalNAc)(2)) for the asialoglycoprotein receptor on parenchymal liver cells. The resulting colchicine-K(GalNAc)(2) conjugate bound to this receptor with an affinity of 4.5 nM. Confocal microscopy studies confirmed rapid uptake and receptor dependency of a prodrug conjugated with fluorescein isothiocyanate. Colchicine-K(GalNAc)(2) substantially increased the transfection efficiency of polyplexed DNA in parenchymal liver cells in a concentration- and receptor-dependent fashion. Colchicine-K(GalNAc)(2) was found to enhance the transfection efficiency by 50-fold at 1 nM, whereas the parental colchicine was ineffective. In conclusion, this nontoxic colchicine-K(GalNAc)(2) conjugate can be a useful tool to improve the transfection efficiency of hepatic nonviral gene transfer vehicles.     

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.     

Plastic micropump with ferrofluidic actuation

We present the realization and characterization of a new type of plastic micropump based on the magnetic actuation of a magnetic liquid. The pump consists of two serial check-valves that convert the periodic motion of a ferrofluidic plug into a pulsed quasi-continuous flow. The ferrofluid is actuated by the mechanical motion of an external NdFeB permanent magnet. The water-based ferrofluid is synthesized in-house using a coprecipitation method and has a saturation magnetization of 32 mT. The micropump consists of various layers of polymethylmethacrylate (PMMA), which are microstructured by powder blasting or by standard mechanical micromachining techniques, and are assembled in a single plastic structure using a monomer gluing solution. Two soft silicone membranes are integrated in the microfluidic structure to form two check-valves. Water has been successfully pumped at flow rates of up to 30 /spl mu/L/min and pumping is achieved at backpressures of up to 25 mbar.     

Influence of cocoa butter refining on the quality of milk chocolate

A refining step is often crucial for the removal of undesired components in fats and oils. More flexible refining technologies are required due to a global decline in cocoa butter quality and to meet industry’s demand for cocoa butters with improved properties. The aim was to investigate the impact of the cocoa butter refining process on milk chocolate quality. Therefore a crude cocoa butter was subjected to a steam refining at different temperatures and this with or without a silica pretreatment. The major effect of the silica pretreatment was the complete removal of phosphorus (thus phospholipids), iron and alkaline components. During the steam refining step mainly Free Fatty Acids (FFA) were removed at increased temperatures (T ? 200 °C). The refining of the cocoa butter influenced the rheological properties of the chocolate. An increased packed column temperature, coinciding with the removal of FFA, resulted in a lower yield stress and a higher viscosity. Reduction of FFA positively influenced the crystallization kinetics and the formation of the crystal network, resulting in differences on a macroscopic scale.     

Effect of activated carbon amendment on bacterial community structure and functions in a PAH impacted urban soil

We collected urban soil samples impacted by polycyclic aromatic hydrocarbons (PAHs) from a sorbent-based remediation field trial to address concerns about unwanted side-effects of 2% powdered (PAC) or granular (GAC) activated carbon amendment on soil microbiology and pollutant biodegradation. After three years, total microbial cell counts and respiration rates were highest in the GAC amended soil. The predominant bacterial community structure derived from denaturing gradient gel electrophoresis (DGGE) shifted more strongly with time than in response to AC amendment. DGGE band sequencing revealed the presence of taxa with closest affiliations either to known PAH degraders, e.g. Rhodococcus jostii RHA-1, or taxa known to harbor PAH degraders, e.g. Rhodococcus erythropolis, in all soils. Quantification by real-time polymerase chain reaction yielded similar dioxygenases gene copy numbers in unamended, PAC-, or GAC-amended soil. PAH availability assessments in batch tests showed the greatest difference of 75% with and without biocide addition for unamended soil, while the lowest PAH availability overall was measured in PAC-amended, live soil. We conclude that AC had no detrimental effects on soil microbiology, AC-amended soils retained the potential to biodegrade PAHs, but the removal of available pollutants by biodegradation was most notable in unamended soil.     

Subset selection from large datasets for Kriging modeling

When building a Kriging model, the general intuition is that using more data will always result in a better model. However, we show that when we have a large non-uniform dataset, using a uniform subset can have several advantages. Reducing the time necessary to fit the model, avoiding numerical inaccuracies and improving the robustness with respect to errors in the output data are some aspects which can be improved by using a uniform subset. We furthermore describe several new and current methods for selecting a uniform subset. These methods are tested and compared on several artificial datasets and one real life dataset. The comparison shows how the selected subsets affect different aspects of the resulting Kriging model. As none of the subset selection methods performs best on all criteria, the best method to choose depends on how the different aspects are valued. The comparison made in this paper can be used to facilitate the user in making a good choice.     

Monolithic micro-direct methanol fuel cell in polydimethylsiloxane with microfluidic channel-integrated Nafion strip

We demonstrate a monolithic polymer electrolyte membrane fuel cell by integrating a narrow (200 μm) Nafion strip in a molded polydimethylsiloxane (PDMS) structure. We propose two designs, based on two 200 μm-wide and two 80 μm-wide parallel microfluidic channels, sandwiching the Nafion strip, respectively. Clamping the PDMS/Nafion assembly with a glass chip that has catalyst-covered Au electrodes, results in a leak-tight fuel cell with stable electrical output. Using 1 M CH₃OH in 0.5 M H₂SO₄ solution as fuel in the anodic channel, we compare the performance of (I) O₂-saturated 0.5 M H₂SO₄ and (II) 0.01 M H₂O₂ in 0.5 M H₂SO₄ oxidant solutions in the cathodic channel. For the 200 μm channel width, the fuel cell has a maximum power density of 0.5 mW cm⁻² and 1.5 mW cm⁻² at room temperature, for oxidants I and II, respectively, with fuel and oxidant flow rates in the 50-160 μL min⁻¹ range. A maximum power density of 3.0 mW cm⁻² is obtained, using oxidant II for the chip with 80 μm-wide channel, due to an improved design that reduces oxidant and fuel depletion effects near the electrodes.     

Measurements of 1/f noise amplitude modulated by a large-signal carrier in bipolar junction transistors

A novel experimental system for the investigation of frequency-translated flicker noise in bipolar junction transistors is demonstrated. First, transistors are characterized for their base–emitter junction behavior and flicker noise parameters in steady state. Then, measurements of the frequency conversion of 1/f noise are performed by the application of a large sinusoidal signal to the base–emitter junctions of bipolar junction transistors. The applied signal is varied in frequency and amplitude, and the resulting conversion gains are reported. A novel measurement technique, which enables the detection of noise fluctuations near a much larger signal is demonstrated. These results are compared with harmonic balance simulation.