From core–shell and Janus structures to tricompartment submicron particles

Titanium dioxide nanoparticles are precisely segregated in or on polymer submicron particles domains by phase separation between a polymer and a hydrophobic liquid or between two different polymers. The inorganic nanoparticles can be located either in the core, as a patch on the surface of the polymer particle, as a disk, or in the middle of Janus polymer particles. In the latter case, tricompartment submicron particles arranged in a linear triblock fashion are fabricated.     

From Isonitriles to Unsaturated NHC Complexes of Gold,Palladium and Platinum

In a modular template synthesis, unsaturated NHC complexes of gold, palladium and platinum were synthesized from simple metal salts, isonitriles and amines with acetal or ketal groups. Upon the addition of amines with tethered acetal or ketal moieties to the metal‐activated isonitrile, first nitrogen acyclic carbene (NAC) complexes are formed. These undergo ring closure and elimination to the unsaturated NHC complexes upon addition of acid. This simple strategy opens an attractive and fast approach to NHC complexes of gold, palladium and platinum. The modular approach allows a fast modification and is well‐suited for the synthesis of unsymetrically and symmetrically substituted unsaturated NHC complexes.

     

Profiling of the Bacterial Microbiota along the Murine Alimentary Tract

Here, the spatial distribution of the bacterial flora along the murine alimentary tract was evaluated using high throughput sequencing in wild-type and Tff3-deficient (Tff3^KO) animals. Loss of Tff3 was linked to increased dextran sodium sulfate-induced colitis. This systematic study shows the results of 13 different regions from the esophagus to the rectum. The number of bacterial species (richness) increased from the esophagus to the rectum, from 50 to 200, respectively. Additionally, the bacterial community structure changed continuously; the highest changes were between the upper/middle and lower gastrointestinal compartments when comparing adjacent regions. Lactobacillus was the major colonizer in the upper/middle gastrointestinal tract, especially in the esophagus and stomach. From the caecum, a drastic diminution of Lactobacillus occurred, while members of Lachnospiraceae significantly increased. A significant change occurred in the bacterial community between the ascending and the transverse colon with Bacteroidetes being the major colonizers with relative constant abundance until the rectum. Interestingly, wild-type and Tff3^KO animals did not show significant differences in their bacterial communities, suggesting that Tff3 is not involved in alterations of intraluminal or adhesive microbiota but is obviously important for mucosal protection, e.g., of the sensitive stem cells in the colonic crypts probably by a mucus plume.     

Druggability Assessment for Selected Serine Proteases in a Pharmaceutical Industry Setting

Target druggability assessment is an integral part of the early target characterization and selection process in pharmaceutical industry. Here, we investigate a set of five different serine proteases from the blood coagulation cascade. The aim of this study is twofold. Firstly, leveraging the wealth of available in-house high-throughput screening (HTS) data, we analyze HTS hit rates and discuss their predictive value for the development of small molecule (SMOL) candidates. Purely structure-activity relationship (SAR) based druggability ratings are compared with computational protein-structure based druggability assessments. Secondly, we evaluate the impact of using conformational ensembles from molecular dynamics (MD) simulations instead of single static crystal structures as basis for computational druggability assessments. Based on this study, we recommend incorporating molecular dynamics routinely into the early target characterization process, especially if only a single X-ray structure is available.     

The Fifth WS/DGAT Enzyme of the Bacterium Marinobacter aquaeolei VT8

Wax esters (WE) belong to the class of neutral lipids. They are formed by an esterification of a fatty alcohol and an activated fatty acid. Dependent on the chain length and desaturation degree of the fatty acid and the fatty alcohol moiety, WE can have diverse physicochemical properties. WE derived from monounsaturated long-chain acyl moieties are of industrial interest due to their very good lubrication properties. Whereas WE were obtained in the past from spermaceti organs of the sperm whale, industrial WE are nowadays mostly produced chemically from fossil fuels. In order to produce WE more sustainably, attempts to produce industrial WE in transgenic plants are steadily increasing. To achieve this, different combinations of WE producing enzymes are expressed in developing Arabidopsis thaliana or Camelina sativa seeds. Here we report the identification and characterization of a fifth wax synthase from the organism Marinobacter aquaeolei VT8, MaWSD5. It belongs to the class of bifunctional wax synthase/acyl-CoA:diacylglycerol O-acyltransferases (WSD). The protein was purified to homogeneity. In vivo and in vitro substrate analyses revealed that MaWSD5 is able to synthesize WE but no triacylglycerols. The protein produces WE from saturated and monounsaturated mid- and long-chain substrates. Arabidopsis thaliana seeds expressing a fatty acid reductase from Marinobacter aquaeolei VT8 and MaWSD5 produce WE. Main WE synthesized are 20:1/18:1 and 20:1/20:1. This makes MaWSD5 a suitable candidate for industrial WE production in planta.     

2‐(1‐Ethynylpyrene)‐Adenosine as a Folding Probe for RNA—Pyrene in or out

A series of short RNA duplexes containing one or two 1‐ethynylpyrene‐modified adenine bases was synthesised. The melting behaviour of these duplexes was examined by monitoring temperature‐dependent pyrene fluorescence. In the singly modified RNA duplexes, the bases flanking the ethynylpyrene‐rA were varied to examine the sequence specificity of the fluorescence change of pyrene upon RNA hybridisation. Because an increase in pyrene fluorescence upon melting of the duplex can be correlated with intercalation of pyrene, and a decrease is usually associated with the position of pyrene outside the strand, a relationship between the flanking bases and the tendency of the dye to intercalate has been established. It was found that pyrene intercalation is less likely to take place if the modified base is flanked only by A–U base pairs. Flanking G–C base pairs, even only in the 5′‐direction of the modified base, will favour intercalation. In addition, we examined a doubly modified compound that had a pyrene located on each strand. The spectra indicated that the two pyrenes were close enough for interaction. Upon melting of the strand, a fluorescence blue shift corresponding to the dissociation of the pyrene–pyrene complex could be observed in addition to the intensity effect already known from the singly modified compounds. Two melting curves based on the different properties of the fluorophore could be extracted, leading to different melting points corresponding to the global duplex melting and to the change of local pyrene environment, respectively.     

Submicron droplet formation in the human lung

The exhaled breath of humans contains droplets originating from the lung lining fluid. An analysis of these droplets for non-volatile proteinaceous biomarkers holds potential as a non-invasive diagnosis of lung diseases. To ease the interpretation of the diagnostic results, the source strength of the particles should be known und therefore an understanding of the particle generation process is required. It is assumed that during reopening of a collapsed terminal airway a liquid bridge of the lung lining fluid ruptures and droplets are generated. The objective of our experimental and theoretical study was to clarify the mechanisms of droplet generation for quiet breathing patterns by investigating in detail the number flux and the particle size distribution in the exhaled breath. The process of liquid film rupture is modelled by computational fluid dynamics analysis from which the droplet size distribution is calculated. In addition the number emission flux and the droplet size distribution are systematically measured in the exhaled breath of healthy volunteers. The strong increase of the particle emission flux with tidal volume and the good agreement between measured and calculated droplet number distribution both showing droplets primarily in the submicron range confirm the present hypothesis that reopening of collapsed airway structures associated with the rupture of a surfactant film is the physical mechanism of droplet generation. This was hypothesized previously in the literature.     

Human Intelligence in the Process of Semantic Content Creation

Despite significant progress over the last years the large-scale adoption of semantic technologies is still to come. One of the reasons for this state of affairs is assumed to be the lack of useful semantic content, a prerequisite for almost every IT system or application using semantics. Through its very nature, this content can not be created fully automatically, but requires, to a certain degree, human contribution. The interest of Internet users in semantics, and in particular in creating semantic content, is, however, low. This is understandable if we think of several characteristics exposed by many of the most prominent semantic technologies, and the applications thereof. One of these characteristics is the high barrier of entry imposed. Interacting with semantic technologies today requires specific skills and expertise on subjects which are not part of the mainstream IT knowledge portfolio. A second characteristic are the incentives that are largely missing in the design of most semantic applications. The benefits of using machine-understandable content are in most applications fully decoupled from the effort of creating and maintaining this content. In other words, users do not have a motivation to contribute to the process. Initiatives in the areas of the Social Semantic Web acknowledged this problem, and identified mechanisms to motivate users to dedicate more of their time and resources to participate in the semantic content creation process. Still, even if incentives are theoretically in place, available human labor is limited and must only be used for those tasks that are heavily dependent on human intervention, and cannot be reliably automated. In this article, we concentrate on this step in between. As a first contribution, we analyze the process of semantic content creation in order to identify those tasks that are inherently human-driven. When building semantic applications involving these specific tasks, one has to install incentive schemes that are likely to encourage users to perform exactly these tasks that crucially rely on manual input. As a second contribution of the article, we propose incentives or incentive-driven tools that can be used to increase user interest in semantic content creation tasks. We hope that our findings will be adopted as recommendations for establishing a fundamentally new form of design of semantic applications by the semantic technologies community.