The accessory bacteriochlorophyll

The primary electron transfer in reaction centers of Rhodobacter sphaeroides is studied by subpicosecond absorption spectroscopy with polarized light in the spectral range of 920-1040 nm. Here the bacteriochlorophyll anion radical has an absorption band while the other pigments of the reaction center have vanishing ground-state absorption. The transient absorption data exhibit a pronounced 0.9-ps kinetic component which shows a strong dichroism. Evaluation of the data yields an angle between the transition moments of the special pair and the species related with the 0.9-ps kinetic component of 26 +/- 8 degrees. This angle compares favorably with the value of 29 degrees expected for the reduced accessory bacteriochlorophyll. Extensive transient absorbance data are fully consistent with a stepwise electron transfer via the accessory bacteriochlorophyll

Influence of the hierarchical architecture of multi-core iron oxide nanoflowers on their magnetic properties

Magnetic properties of superparamagnetic iron oxide nanoparticles are controlled mainly by their particle size and by their particle size distribution. Magnetic properties of multi-core iron oxide nanoparticles, often called iron oxide nanoflowers (IONFs), are additionally affected by the interaction of magnetic moments between neighboring cores. The knowledge about the hierarchical structure of IONFs is therefore essential for understanding the magnetic properties of IONFs. In this contribution, the architecture of multi-core IONFs was investigated using correlative multiscale transmission electron microscopy (TEM), X-ray diffraction and dynamic light scattering. The multiscale TEM measurements comprised low-resolution and high-resolution imaging as well as geometric phase analysis. The IONFs contained maghemite with the average chemical composition -Fe$_{2.72±0.02}$O$_{4}$. The metallic vacancies located on the octahedral lattice sites of the spinel ferrite structure were partially ordered. Individual IONFs consisted of several cores showing frequently a specific crystallographic orientation relationship between direct neighbors. This oriented attachment may facilitate the magnetic alignment within the cores. Individual cores were composed of partially coherent nanocrystals having almost the same crystallographic orientation. The sizes of individual constituents revealed by the microstructure analysis were correlated with the magnetic particle sizes that were obtained from fi

Continuous size fractionation of magnetic nanoparticles by using simulated moving bed chromatography

The size fractionation of magnetic nanoparticles is a technical problem, which until today can only be solved with great effort. Nevertheless, there is an important demand for nanoparticles with sharp size distributions, for example for medical technology or sensor technology. Using magnetic chromatography, we show a promising method for fractionation of magnetic nanoparticles with respect to their size and/or magnetic properties. This was achieved by passing magnetic nanoparticles through a packed bed of fine steel spheres with which they interact magnetically because single domain ferro-/ferrimagnetic nanoparticles show a spontaneous magnetization. Since the strength of this interaction is related to particle size, the principle is suitable for size fractionation. This concept was transferred into a continuous process in this work using a so-called simulated moving bed chromatography. Applying a suspension of magnetic nanoparticles within a size range from 20 to 120 nm, the process showed a separation sharpness of up to 0.52 with recovery rates of 100%. The continuous feed stream of magnetic nanoparticles could be fractionated with a space-time-yield of up to 5 mg/(L·min). Due to the easy scalability of continuous chromatography, the process is a promising approach for the efficient fractionation of industrially relevant amounts of magnetic nanoparticles

Extending pathways based on gene lists using InterPro domain signatures

<p>Abstract</p> <p>Background</p> <p>High-throughput technologies like functional screens and gene expression analysis produce extended lists of candidate genes. Gene-Set Enrichment Analysis is a commonly used and well established technique to test for the statistically significant over-representation of particular pathways. A shortcoming of this method is however, that most genes that are investigated in the experiments have very sparse functional or pathway annotation and therefore cannot be the target of such an analysis. The approach presented here aims to assign lists of genes with limited annotation to previously described functional gene collections or pathways. This works by comparing InterPro domain signatures of the candidate gene lists with domain signatures of gene sets derived from known classifications, e.g. KEGG pathways.</p> <p>Results</p> <p>In order to validate our approach, we designed a simulation study. Based on all pathways available in the KEGG database, we create test gene lists by randomly selecting pathway genes, removing these genes from the known pathways and adding variable amounts of noise in the form of genes not annotated to the pathway. We show that we can recover pathway memberships based on the simulated gene lists with high accuracy. We further demonstrate the applicability of our approach on a biological example.</p> <p>Conclusion</p> <p>Results based on simulation and data analysis show that domain based pathway enrichment analysis is a very sensitive method to test for enrichment of pathways in sparsely annotated lists of genes. An R based software package <it>domainsignatures</it>, to routinely perform this analysis on the results of high-throughput screening, is available via Bioconductor.</p

Statistical methods and software for the analysis of highthroughput reverse genetic assays using flow cytometry readouts

Highthroughput cell-based assays with flow cytometric readout provide a powerful technique for identifying components of biologic pathways and their interactors. Interpretation of these large datasets requires effective computational methods. We present a new approach that includes data pre-processing, visualization, quality assessment, and statistical inference. The software is freely available in the Bioconductor package prada. The method permits analysis of large screens to detect the effects of molecular interventions in cellular systems

Spectroscopic characterization of reaction centers of the (M)Y210W mutant of the photosynthetic bacterium Rhodobacter sphaeroides

The tyrosine-(M)210 of the reaction center of Rhodobacter sphaeroides 2.4.1 has been changed to a tryptophan using site-directed mutagenesis. The reaction center of this mutant has been characterized by low-temperature absorption and fluorescence spectroscopy, time-resolved sub-picosecond spectroscopy, and magnetic resonance spectroscopy. The charge separation process showed bi-exponential kinetics at room temperature, with a main time constant of 36 ps and an additional fast time constant of 5.1 ps. Temperature dependent fluorescence measurements predict that the lifetime of P* becomes 4–5 times slower at cryogenic temperatures. From EPR and absorbance-detected magnetic resonance (ADMR, LD-ADMR) we conclude that the dimeric structure of P is not significantly changed upon mutation. In contrast, the interaction of the accessory bacteriochlorophyll BA with its environment appears to be altered, possibly because of a change in its position

A novel production route and process optimization of biomass-derived paraffin wax for pharmaceutical application

The Biomass to Liquid (BtL) Fischer-Tropsch (FT) route converts lignocellulosic feedstock to renewable hydrocarbons. This, paper shows a novel production route for biomass-derived synthetic paraffin wax via gasification of lignocellulosic feedstock, Fischer-Tropsch synthesis (FTS) and hydrofining. The Fischer-Tropsch wax was fractionated, refined and analyzed with respect to compliance to commercial standards. The fractioned paraffin waxes were hydrofined using a commercial sulfide NiMo–Al2O3 catalyst and a trickle bed reactor. A parametric variation was performed to optimize the hydrofining process. It was shown that the produced medium-melt paraffin wax could fulfill the requirements for “Paraffinum solidum” defined by the European Pharmacopoeia (Ph. Eur). The high-melt wax fraction showed potential to be used as food packaging additive. Furthermore, the renewable wax was analyzed regarding PAH content and it was shown that the hydrofined wax was quasi-PAH-free

IEX-1 directly interferes with RelA/p65 dependent transactivation and regulation of apoptosis

The early response gene IEX-1 plays a complex role in the regulation of apoptosis. Depending on the cellular context and the apoptotic stimulus, IEX-1 is capable to either enhance or suppress apoptosis. To further dissect the molecular mechanisms involved in the modulation of apoptosis by IEX-1, we analysed the molecular crosstalk between IEX-1 and the NF-kappa B pathway. Using GST-pulldown assays, a direct interaction of IEX-1 with the C-terminal region of the subunit RelA/p65 harbouring the transactivation domain of the NF-kappa B transcription factor was shown. This interaction negatively regulates RelA/p65 dependent transactivation as shown by GAL4-and luciferase assay and was confirmed for the endogenous proteins by co-immunoprecipitation experiments. Using deletion constructs, we were able to map the C-terminal region of IEX-1 as the critical determinant of the interaction with RelA/p65. We could further show, that IEX-1 mediated NF-kappa B inhibition accounts for the reduced expression of the anti-apoptotic NF-kappa B target genes Bc1-2, Bcl-xL, cIAP1 and cIAP2, thereby sensitizing cells for apoptotic stimuli. Finally, ChIP-assays revealed that IEX-1 associates with the promoter of these genes. Altogether, our findings suggest a critical role of IEX-1 in the NF-kappa B dependent regulation of apoptotic responses. (C) 2007 Elsevier B.V All rights reserved

Residue concentrations of cloxacillin in milk after intramammary dry cow treatment considering dry period length

Dry cow treatment with an intramammary antibiotic is recommended to reduce the risk of mastitis at the beginning of the next lactation. The dry period may be shortened unintentionally, affecting antibiotic residue depletion and the time when residues reach concentrations below the maximum residue limit (MRL). The objective of this study was to evaluate residue depletion in milk after dry cow treatment with cloxacillin, considering dry periods of 14 (G14d), 21 (G21d), and 28 d (G28d). Overall, fifteen cows with 60 udder quarters were included in the study. For each cow, three of the udder quarters were treated with 1000 mg cloxacillin benzathine (2:1) on d 252, d 259, and d 266 of gestation; one quarter was left untreated. Milk samples were drawn until 20 DIM and milk composition, somatic cell count and cloxacillin residues were analyzed. The HPLC-MS/MS revealed different excretion kinetics for the compounds cloxacillin and cloxacillin benzathine (1:1). All cows showed a cloxacillin and cloxacillin benzathine (1:1) concentration below the MRL of 30 µg/kg after 5 d. In the udder quarters of G21d and G28d, the cloxacillin concentration was already below the MRL at first milking after calving. The cloxacillin benzathine (1:1) concentration in the milk of G28d, G21d, and G14d fell below 30 µg/kg on the 5th, 3rd, and 5th DIM, respectively. Shortening the dry period affects residue depletion after dry cow treatment with cloxacillin. The risk of exceeding the MRL, however, seems low, even with dry periods shorter than 14 d

Peptide Fingerprinting of Alzheimer's Disease in Cerebrospinal Fluid: Identification and Prospective Evaluation of New Synaptic Biomarkers

&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; Today, dementias are diagnosed late in the course of disease. Future treatments have to start earlier in the disease process to avoid disability requiring new diagnostic tools. The objective of this study is to develop a new method for the differential diagnosis and identification of new biomarkers of Alzheimer's disease (AD) using capillary-electrophoresis coupled to mass-spectrometry (CE-MS) and to assess the potential of early diagnosis of AD.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Methods and Findings:&lt;/b&gt; Cerebrospinal fluid (CSF) of 159 out-patients of a memory-clinic at a University Hospital suffering from neurodegenerative disorders and 17 cognitively-healthy controls was used to create differential peptide pattern for dementias and prospective blinded-comparison of sensitivity and specificity for AD diagnosis against the Criterion standard in a naturalistic prospective sample of patients. Sensitivity and specificity of the new method compared to standard diagnostic procedures and identification of new putative biomarkers for AD was the main outcome measure. CE-MS was used to reliably detect 1104 low-molecular-weight peptides in CSF. Training-sets of patients with clinically secured sporadic Alzheimer's disease, frontotemporal dementia, and cognitively healthy controls allowed establishing discriminative biomarker pattern for diagnosis of AD. This pattern was already detectable in patients with mild cognitive impairment (MCI). The AD-pattern was tested in a prospective sample of patients (n = 100) and AD was diagnosed with a sensitivity of 87% and a specificity of 83%. Using CSF measurements of beta-amyloid1-42, total-tau, and phospho(181)-tau, AD-diagnosis had a sensitivity of 88% and a specificity of 67% in the same sample. Sequence analysis of the discriminating biomarkers identified fragments of synaptic proteins like proSAAS, apolipoprotein J, neurosecretory protein VGF, phospholemman, and chromogranin A.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; The method may allow early differential diagnosis of various dementias using specific peptide fingerprints and identification of incipient AD in patients suffering from MCI. Identified biomarkers facilitate face validity for the use in AD diagnosis.&lt;/p&gt