Capillary Rise in Nanopores: Molecular Dynamics Evidence for the Lucas-Washburn Equation

When a capillary is inserted into a liquid, the liquid will rapidly flow into it. This phenomenon, well studied and understood on the macroscale, is investigated by Molecular Dynamics simulations for coarse-grained models of nanotubes. Both a simple Lennard-Jones fluid and a model for a polymer melt are considered. In both cases after a transient period (of a few nanoseconds) the meniscus rises according to a $\sqrt{\textrm{time}}$-law. For the polymer melt, however, we find that the capillary flow exhibits a slip length $\delta$, comparable in size with the nanotube radius $R$. We show that a consistent description of the imbibition process in nanotubes is only possible upon modification of the Lucas-Washburn law which takes explicitly into account the slip length $\delta$.Comment: 4 pages 4 figure

Immersed superhydrophobic surfaces: Gas exchange, slip and drag reduction properties

Superhydrophobic surfaces combine high aspect ratio micro- or nano-topography and hydrophobic surface chemistry to create super water-repellent surfaces. Most studies consider their effect on droplets, which ball-up and roll-off. However, their properties are not restricted to modification of the behaviour of droplets, but potentially influence any process occurring at the solid-liquid interface. Here, we highlight three recent developments focused on the theme of immersed superhydrophobic surfaces. The first illustrates the ability of a superhydrophobic surface to act as a gas exchange membrane, the second demonstrates a reduction in drag during flow through small tubes and the third considers a macroscopic experiment demonstrating an increase in the terminal velocity of settling spheres

Phase transitions in biological membranes

Native membranes of biological cells display melting transitions of their lipids at a temperature of 10-20 degrees below body temperature. Such transitions can be observed in various bacterial cells, in nerves, in cancer cells, but also in lung surfactant. It seems as if the presence of transitions slightly below physiological temperature is a generic property of most cells. They are important because they influence many physical properties of the membranes. At the transition temperature, membranes display a larger permeability that is accompanied by ion-channel-like phenomena even in the complete absence of proteins. Membranes are softer, which implies that phenomena such as endocytosis and exocytosis are facilitated. Mechanical signal propagation phenomena related to nerve pulses are strongly enhanced. The position of transitions can be affected by changes in temperature, pressure, pH and salt concentration or by the presence of anesthetics. Thus, even at physiological temperature, these transitions are of relevance. There position and thereby the physical properties of the membrane can be controlled by changes in the intensive thermodynamic variables. Here, we review some of the experimental findings and the thermodynamics that describes the control of the membrane function.Comment: 23 pages, 15 figure

pcrEfficiency: a Web tool for PCR amplification efficiency prediction

<p>Abstract</p> <p>Background</p> <p>Relative calculation of differential gene expression in quantitative PCR reactions requires comparison between amplification experiments that include reference genes and genes under study. Ignoring the differences between their efficiencies may lead to miscalculation of gene expression even with the same starting amount of template. Although there are several tools performing PCR primer design, there is no tool available that predicts PCR efficiency for a given amplicon and primer pair.</p> <p>Results</p> <p>We have used a statistical approach based on 90 primer pair combinations amplifying templates from bacteria, yeast, plants and humans, ranging in size between 74 and 907 bp to identify the parameters that affect PCR efficiency. We developed a generalized additive model fitting the data and constructed an open source Web interface that allows the obtention of oligonucleotides optimized for PCR with predicted amplification efficiencies starting from a given sequence.</p> <p>Conclusions</p> <p>pcrEfficiency provides an easy-to-use web interface allowing the prediction of PCR efficiencies prior to web lab experiments thus easing quantitative real-time PCR set-up. A web-based service as well the source code are provided freely at <url>http://srvgen.upct.es/efficiency.html</url> under the GPL v2 license.</p

DONSON and FANCM associate with different replisomes distinguished by replication timing and chromatin domain

Eukaryotic replisomes are multiprotein complexes. Here the authors reveal two distinct stressed replisomes, associated with DONSON and FANCM, displaying a bias in replication timing and chromatin domain

Purification, characterization, and cloning of a bifunctional molybdoenzyme with hydratase and alcohol dehydrogenase activity

A bifunctional hydratase/alcohol dehydrogenase was isolated from the cyclohexanol degrading bacterium Alicycliphilus denitrificans DSMZ 14773. The enzyme catalyzes the addition of water to α,β-unsaturated carbonyl compounds and the subsequent alcohol oxidation. The purified enzyme showed three subunits in SDS gel, and the gene sequence revealed that this enzyme belongs to the molybdopterin binding oxidoreductase family containing molybdopterins, FAD, and iron-sulfur clusters

A very interesting traditional method in the treatment of skin lesions: aqua regia and related complications

BACKGROUND: Aqua regia, a highly corrosive mixture of concentrated nitric acid and hydrochloric acid, is used to dissolve various metals such as gold and platinum that are not soluble in other types of acids. For the first time in the literature, we report the adverse effects that were observed following the utilization of this strong acid solution in the treatment of various skin lesions. METHODS: Between 2010 and 2013, 43 patients (55.8 % female) with a mean age of 40.2 years, were admitted to our hospital for scars, wounds or malign lesions related to the use of aqua regia on skin lesions. Sixteen patients reported to use aqua regia for treating wounds and 27 of them used it for their scars. RESULTS: Out of 43 patients, 9 patients developed necrosis, 12 had hypertrophic scars, 15 had scars and 7 had non-healing wounds resembling malignant lesions. The non-healing wounds were located in the facial region in five patients, in the cervical region in one and on the finger-tip in another. Histopathological examination of these non-healing wounds revealed basal and squamous cell carcinoma. The patients were admitted to the plastic surgery department approximately 6–24 months after aqua regia application with complaints of growing lesions. Secondary healing in the lesions with scar development in 55 % of the patients is an acceptable result. However, 27 % of the patients with hypertrophic scars and 16 % of the patients with malignant lesions required intervention. CONCLUSION: This present study showed that non-medical alternative treatments have major risks. Aqua regia application might have resulted in the development or rapid progression of malignant tumours in seven patients. In the literature, it has been reported that a number of physical traumas may cause skin cancer. Based on this information, the possibility of such an effect of aqua regia cannot be excluded

RNA metabolism is the primary target of formamide in vivo

The synthesis, processing and function of coding and non-coding RNA molecules and their interacting proteins has been the focus of a great deal of research that has boosted our understanding of key molecular pathways that underlie higher order events such as cell cycle control, development, innate immune response and the occurrence of genetic diseases. In this study, we have found that formamide preferentially weakens RNA related processes in vivo. Using a non-essential Schizosaccharomyces pombe gene deletion collection, we identify deleted loci that make cells sensitive to formamide. Sensitive deletions are significantly enriched in genes involved in RNA metabolism. Accordingly, we find that previously known temperature-sensitive splicing mutants become lethal in the presence of the drug under permissive temperature. Furthermore, in a wild type background, splicing efficiency is decreased and R-loop formation is increased in the presence of formamide. In addition, we have also isolated 35 formamide-sensitive mutants, many of which display remarkable morphology and cell cycle defects potentially unveiling new players in the regulation of these processes. We conclude that formamide preferentially targets RNA related processes in vivo, probably by relaxing RNA secondary structures and/or RNA-protein interactions, and can be used as an effective tool to characterize these processes

Surface Hardness Impairment of Quorum Sensing and Swarming for Pseudomonas aeruginosa

The importance of rhamnolipid to swarming of the bacterium Pseudomonas aeruginosa is well established. It is frequently, but not exclusively, observed that P. aeruginosa swarms in tendril patterns—formation of these tendrils requires rhamnolipid. We were interested to explain the impact of surface changes on P. aeruginosa swarm tendril development. Here we report that P. aeruginosa quorum sensing and rhamnolipid production is impaired when growing on harder semi-solid surfaces. P. aeruginosa wild-type swarms showed huge variation in tendril formation with small deviations to the “standard” swarm agar concentration of 0.5%. These macroscopic differences correlated with microscopic investigation of cells close to the advancing swarm edge using fluorescent gene reporters. Tendril swarms showed significant rhlA-gfp reporter expression right up to the advancing edge of swarming cells while swarms without tendrils (grown on harder agar) showed no rhlA-gfp reporter expression near the advancing edge. This difference in rhamnolipid gene expression can be explained by the necessity of quorum sensing for rhamnolipid production. We provide evidence that harder surfaces seem to limit induction of quorum sensing genes near the advancing swarm edge and these localized effects were sufficient to explain the lack of tendril formation on hard agar. We were unable to artificially stimulate rhamnolipid tendril formation with added acyl-homoserine lactone signals or increasing the carbon nutrients. This suggests that quorum sensing on surfaces is controlled in a manner that is not solely population dependent

Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium

Clostridium autoethanogenum is an acetogenic bacterium capable of producing high value commodity chemicals and biofuels from the C1 gases present in synthesis gas. This common industrial waste gas can act as the sole energy and carbon source for the bacterium that converts the low value gaseous components into cellular building blocks and industrially relevant products via the action of the reductive acetyl-CoA (Wood-Ljungdahl) pathway. Current research efforts are focused on the enhancement and extension of product formation in this organism via synthetic biology approaches. However, crucial to metabolic modelling and directed pathway engineering is a reliable and comprehensively annotated genome sequence