4,4-Dimethyl-4-silapentane-1-ammonium trifluoroacetate (DSA), a promising universal internal standard for NMR-based metabolic profiling studies of biofluids, including blood plasma and serum

Nuclear magnetic resonance (NMR)-based metabolic profiling of biofluids and tissues are of key interest to enhance biomarker discovery for disease, drug efficacy and toxicity studies. Urine and blood plasma/serum are the biofluids of most interest as they are the most accessible in both clinical and preclinical studies. However, proteinaceous fluids, such as blood serum or plasma, represent the greatest technical challenge since the chemical shift (δ) and line-width (ν_1/2) of internal standards currently used for aqueous NMR samples are greatly affected by protein binding. We have therefore investigated the suitability of 4,4-dimethyl-4-silapentane-1-ammonium trifluoroacetate (DSA) as a universal internal standard for biofluids. Proton (¹H) NMR spectroscopy was used to determine the effect of serum pH (3, 7.4 and 10) and DSA concentration on the overall lineshape and position of the trimethylsilyl resonance of DSA. The results were compared to that of 3-(trimethylsilyl)propionic acid sodium salt (TSP). Both the chemical shift and line-width of the DSA peak were not significantly affected by pH or DSA concentration, whereas these parameters for TSP showed large variations due to protein binding. Furthermore, the peak area of DSA correlated linearly with its concentration under all pH conditions, whilst no linear correlation was observed with TSP. Overall, in contrast to TSP, these results support the use of DSA as an accurate universal internal chemical shift reference and concentration/normalisation standard for biofluids. In the case of proteinaceous biofluids such as serum, where no current standard is available, this offers a considerable saving in both operator and spectrometer time.     

Heterarchy in biological systems: a logic-based dynamical model of abstract biological network derived from time-state-scale re-entrant form

Heterarchical structure is important for understanding robustness and evolvability in a wide variety of levels of biological systems. Although many studies emphasize the heterarchical nature of biological systems, only a few computational representations of heterarchy have been created thus far. We propose here the time-state-scale re-entrant form to address the self-referential property derived from setting heterarchical structure. In this paper, we apply the time-state-scale re-entrant form to abstract self-referential modeling for a functional manifestation of biological network presented by [Tsuda, I., Tadaki, K., 1997. A logic-based dynamical theory for a genesis of biological threshold. BioSystems 42, 45-64]. The numerical results of this system show different intermittent phase transitions and power-law distribution of time spent in activating functional manifestation. The Hierarchically separated time-scales obtained from spectrum analysis imply that the reactions at different levels simultaneously appear in a dynamical system. The results verify the mutual inter-relationship between heterarchical structure in biological systems and the self-referential property of computational heterarchical systems.     

Swelling behaviour of alginate–chitosan microcapsules prepared by external gelation or internal gelation technology

Swelling behaviour is one of the important properties for microcapsules made by hydrogels, which always affects the diffusion and release of drugs when the microcapsules are applied in drug delivery systems. In this paper, alginate–chitosan microcapsules were prepared by different technologies called external or internal gelation process respectively. With the volume swelling degree (S_w) as an index, the effect of properties of chitosan on the swelling behaviour of both microcapsules was investigated. It was demonstrated that the microcapsules with low molecular weight and high concentration of chitosan gave rise to low S_w. Considering the need of maintaining drug activity and drug loading, neutral pH and short gelation time were favorable. It was also noticed that S_w of internal gelation microcapsules was lower than that of external gelation microcapsules, which was interpreted by the structure analysis of internal or external gelation Ca–alginate beads with the aid of confocal laser scanning microscope.     

Restoring natural seepage conditions on former agricultural grasslands does not lead to reduction of organic matter decomposition and soil nutrient dynamics

In the central part of the Netherlands, wetland restoration projects involve the rewetting of former agricultural land, where low water levels were artificially maintained (polders). Many of these projects do not result in the expected reduction of nitrogen and phosphorus availability and subsequent re-establishment of a diverse wetland vegetation. The aim of the present study was to investigate which mechanisms are responsible for this lack of success. Thereto, we studied the effect of rewetting of former agricultural grasslands on acidified peat soil (pH = 3.5) on organic matter decomposition, nitrogen cycling and phosphorus availability in the soil for three seasons. To provide an explanation for the observed effects, we simultaneously studied a set of potentially controlling abiotic soil conditions that were expected to change after rewetting. It was found that rewetting of these grasslands with natural, unpolluted seepage water did not affect nitrogen cycling, but raised decomposition rates and almost doubled phosphorus availability. The main cause of these effects is a raise of soil pH to about 7 due to the hydrochemical composition of the soil pore water after rewetting, which reflects groundwater with high amounts of buffering ions. This effect overruled any reduction in process rates by the lowered soil redox potential. The counterintuitive finding of eutrophication after rewetting with natural and unpolluted water is considered to represent a new form of internal eutrophication, triggered by the restoration of natural site conditions of former agricultural land on acid peat soil.     

Ectopic expression of eIF4E-transporter triggers the movement of eIF4E into P-bodies, inhibiting steady-state translation but not the pioneer round of translation

Nonsense-mediated mRNA decay (NMD) is the best-characterized mRNA surveillance mechanism; this process removes faulty mRNAs harboring premature termination codons (PTCs). NMD targets newly synthesized mRNAs bound by nuclear cap-binding proteins 80/20 (CBP80/20) and exon junction complex (EJC), the former of which is thought to recruit the ribosome to initiate the pioneer round of translation. After completion of the pioneer round of translation, CBP80/20 is replaced by the cytoplasmic cap-binding protein eIF4E, which mediates steady-state translation in the cytoplasm. Here, we show that overexpression of eIF4E-T preferentially inhibits cap-dependent steady-state translation, but not the pioneer round of translation. We also demonstrate that overexpression of eIF4E-T or Dcp1a triggers the movement of eIF4E into the processing bodies. These results suggest that the pioneer round of translation differs from steady-state translation in terms of ribosome recruitment.     

The Büdöskút Olistolith,an exotic limestone block from the Bükk mountains (NE-Hungary)

Summary The present paper presents results of stratigraphical, sedimentological and micropalaeontological investigations of an olistolith from the Büd?skút area in the Bükk Mts (NW Hungary). The olistolith consists of Norian sub- and peritidal platform carbonates (Büd?skút lime-stone). During early diagenesis dissolution cavities originated which where filled by ostracodal mudstones. Other cavities first were wallpapered by evinospongial crusts and later filled either by ostracodal mudstones or by brick-red haematitic material (weathered bauxite). The evinospongial crusts show stromatolite-like structures and their forming therefore is supposed to be organically (microbially) induced. During the Early up to the Late Jurassic the host rock was dissected by neptunian dykes. The internal sediment's faunal content reveals that the dykes formed during the (?) Hettangian/Sinemurian and the Toarcian— Oxfordian age. A comparison of the Büd?skút limestone neptunian dyke internal sediments with the Bükk parautochthonous and the Szarvasko-Mónosbél nappe complex sedimentary columns shows no similarities. Therefore the Büd?skút olistolith is interpreted as an exotic body within the Bükk Mts.     

Isolation and PCR detection of <Emphasis Type="Italic">Enterobacter sakazakii</Emphasis> in South African food products,specifically infant formula milks

Enterobacter sakazakii has recently been identified as an opportunistic pathogen. The current culture-dependent detection methods for these bacteria are time-consuming and in this study a PCR method for the detection of E. sakazakii in South African food products, including an internal amplification control (IAC) was developed. DNA was isolated and amplified from the products and they were plated on selective growth media after pre-enrichment and enrichment in Enterobacteriaceae enrichment broth. Four of the 22 products tested positive for the presence of E. sakazakii, confirmed by PCR detection and growth on selective media. The PCR method proved effective in detecting E. sakazakii in South African products after three days and could serve as an alternative for traditional microbiological techniques.     

FIM Imaging and FIMtrack: Two New Tools Allowing High-throughput and Cost Effective Locomotion Analysis

The analysis of neuronal network function requires a reliable measurement of behavioral traits. Since the behavior of freely moving animals is variable to a certain degree, many animals have to be analyzed, to obtain statistically significant data. This in turn requires a computer assisted automated quantification of locomotion patterns. To obtain high contrast images of almost translucent and small moving objects, a novel imaging technique based on frustrated total internal reflection called FIM was developed. In this setup, animals are only illuminated with infrared light at the very specific position of contact with the underlying crawling surface. This methodology results in very high contrast images. Subsequently, these high contrast images are processed using established contour tracking algorithms. Based on this, we developed the FIMTrack software, which serves to extract a number of features needed to quantitatively describe a large variety of locomotion characteristics. During the development of this software package, we focused our efforts on an open source architecture allowing the easy addition of further modules. The program operates platform independent and is accompanied by an intuitive GUI guiding the user through data analysis. All locomotion parameter values are given in form of csv files allowing further data analyses. In addition, a Results Viewer integrated into the tracking software provides the opportunity to interactively review and adjust the output, as might be needed during stimulus integration. The power of FIM and FIMTrack is demonstrated by studying the locomotion of Drosophila larvae.     

Medial prefrontal cortex dissociation between self and others in a referential task: An fMRI study based on word traits

A number of recent neuroimaging studies using self referential tasks have investigated whether self referential processing depends on a unique neural basis that operates specifically in the medial prefrontal cortex. However, these studies have provided contradictory results despite the use of similar methodologies. We hypothesized that these discrepancies are partially related to the task-difficulty that presents dissociations reaction times in the self- and other-referential tasks. We therefore measured brain activity during self and other referential tasks to determine if such activity can be dissociated according to the reaction times (fast versus slow) for the trait words. Activation differed across self and other only in the slow word condition. The self referential condition with slow reaction time produced greater activation in the ventromedial prefrontal cortex, whereas the other referential condition with slow reaction time produced activation of the middle temporal gyrus. Results suggested that the task-difficulty might affect whether or not brain activities within MPFC would be dissociated between self- and other-referential processing.