Microbial pretreatment of coals: A tool for solubilization of lignite in organic solvent – quinoline

A method was developed for the conversion of low rank coals to products soluble in an organic solvent (quinoline). A selected group of polynuclear aromatic-compound-degrading and lignin-degrading facultative pure cultures and enriched anaerobic mixed microbial cultures developed for this purpose were used separately as well as together under co-culture conditions for stepwise treatment of Neyveli lignite (NL). This aerobic-anaerobic co-metabolic (co-culture) biodegradation (AACB) process resulted in the enhancement of quinoline extractability of the lignite, thereby yielding clean coal substance (the extract). The residual lignite obtained after quinoline extraction was subjected to a second step of AACB fermentation treatment. This resulted in further extraction of lignite in quinoline. The conditions were optimised for AACB fermentation treatment. The two-step AACB fermentation process under optimum conditions, resulted in an overall enhancement of yield of extract from 18% for the original lignite sample to 56% for the treated sample. The changes in the filtrate were evaluated using UV spectra, those in the residue were evaluated using FTIR spectroscopy and UV-reflectance and those in the extract using proton NMR spectra of the chloroform soluble fraction. The results indicated a decreased absorption in the carbonyl region in the AACB-treated residue and also a decrease in the overall mineral matter in the lignite samples. The mechanism of the AACB fermentation process is discussed. The process affords biosolubilization of lignite in organic solvent (quinoline) under milder conditions along with a simultaneous removal of a part of the mineral matter present in the coal. Uses for the clean coal extract obtained are suggested.     

AutoCellRow (ACR) – A new tool for the automatic quantification of cell radial files in conifer images

Quantitative wood anatomy (QWA) is a growing field of dendrochronology that allows obtaining a large number of parameters as the number, size and spatial arrangement of cellular elements, elements that highlight the adjustments of trees to their environment. In this work, we presented the free/libre open-source software AutoCellRow (ACR), a ready-to-use tool for automatic QWA in conifers. The ACR analyzes radial files of cells on cross-sections views of tree rings and provides automatic measurements of different cell parameters (e.g., lumen radial diameter, double cell wall thickness and cell radial diameter) for each cell along the selected radial file. The ACR measurements are based on high performed image analysis of xylem cells. The accuracy of the software measurements was tested in cross-sections of five conifer species from a semi-arid area of southern Siberia, and compared with measurements obtained by a semiautomatic tool. Our results suggested high accuracy in the ACR cell traits measurements, facilitating and speeding the analysis of quantitative wood anatomy in conifers over radial files of cells.     

Development and validation of a serological potency test for the release of Leptospira vaccines – Requirements in the European Union

Both European Pharmacopoeia Monograph 01/2008:0447 “Canine Leptospirosis vaccine (inactivated)” and the more recent Monograph 01/2008:1939 “Bovine Leptospirosis vaccine (inactivated)” explicitly allow for a sero-response test to assess batch potency. Test setup and requirements for in vivo and in vitro validation are described. Furthermore, the two main strategies to assess batch potency and their specific demands are addressed.     

Hydrophilicity Matching – A Potential Prerequisite for the Formation of Protein-Protein Complexes in the Cell

A binding event between two proteins typically consists of a diffusional search of binding partners for one another, followed by a specific recognition of the compatible binding sites resulting in the formation of the complex. However, it is unclear how binding partners find each other in the context of the crowded, constantly fluctuating, and interaction-rich cellular environment. Here we examine the non-specific component of protein-protein interactions, which refers to those physicochemical properties of the binding partners that are independent of the exact details of their binding sites, but which can affect their localization or diffusional search for one another. We show that, for a large set of high-resolution experimental 3D structures of binary, transient protein complexes taken from the DOCKGROUND database, the binding partners display a surprising, statistically significant similarity in terms of their total hydration free energies normalized by a size-dependent variable. We hypothesize that colocalization of binding partners, even within individual cellular compartments such as the cytoplasm, may be influenced by their relative hydrophilicity, potentially in response to local hydrophilic gradients.     

Image guidance in clinical practice – Influence of positioning inaccuracy on the dose distribution for prostate cancer

BackgroundIn order to consider potential positioning errors there are different recipes for safety-margins for CTV-to-PTV expansion. The aim of this study is to simulate the effect of positioning inaccuracy with clinically realistic patient treatment plans.MethodsFor a collective of 40 prostate patients, the isocenter was shifted back appropriately to the applied table shifts after positioning verification, simulating that no positioning correction had been performed and the treatment plans were recalculated. All the treatment fractions with the appropriate isocenter-shifts were added to yield a new plan considering two scenarios:

• 1)Extreme scenario: summation of only shifted plans.
• 2)Realistic scenario: consideration of the original treatment plan for the fractions with verification imaging.

Afterwards all plans were analysed and compared with each other regarding target coverage, sparing of organs at risk (OAR) and normal tissue complication probability (NTCP).ResultsDose distributions and especially DVH show a deterioration of the target-coverage caused by the positioning inaccuracy. Deviations in dose at a single point can reach values of over 10 Gy. In single cases minimum plan agreement only achieved 66% pass within 3% local dose for the realistic case. Organs at risk and NTCP analysis result in a slightly better sparing of the rectum. Measures of quality like homogeneity and conformity differ just minimally regarding the different scenarios.ConclusionPTV-coverage suffers markedly by the positioning uncertainties, the shifted plans are in large parts clinically not acceptable. Surprisingly sparing of the OAR is not negatively affected by potential positioning errors for this prostate collective.     

Network genomics – A novel approach for the analysis of biological systems in the post-genomic era

Network Genomics studies genomics and proteomics foundations of cellular networks in biological systems. It complements systems biology in providing information on elements, their interaction and their functional interplay in cellular networks. The relationship between genomic and proteomic high-throughput technologies and computational methods are described, as well as several examples of specific network genomic application are presented.     

Fourth meeting of the European Network of Research Tissue Banks – Future strategy to increase collaborations in the supply of human tissue for biomedical research

This report records the Fourth meeting of the European Network of Research Tissue Bank (Brussels, 18th March 2004) which was attended by Mel Read MEP. The existing membership of this informal group represents European Human Research Tissue Bankers, biomedical researchers seeking access to human tissue and allied groups including animal welfare representatives. This Fourth meeting provided a forum to update members on individual activity in this area. A particular focus of this meeting was to consider the status of this group and future affiliations to increase the profile and activity of this Network. This meeting addressed differences in legislative and ethical requirements governing the use of human tissue in biomedical research in the different countries represented. Future activity of the ENRTB, planned at this meeting, will target harmonisation of current differences which are currently barriers to increased access to human tissue for biomedical research. Through the harmonisation of procurement, processing and distribution of human tissue specimens the ENRTB will provide a mechanism to benefit human health through increased use of human tissue in pharmacotoxicological studies and the associated replacement of animal tests.     

Identification of PrP sequences essential for the interaction between the PrP polymers and Aβ peptide in a yeast-based assay

Alzheimer disease is associated with the accumulation of oligomeric amyloid β peptide (Aβ), accompanied by synaptic dysfunction and neuronal death. Polymeric form of prion protein (PrP), PrP^Sc, is implicated in transmissible spongiform encephalopathies (TSEs). Recently, it was shown that the monomeric cellular form of PrP (PrP^C), located on the neuron surface, binds Aβ oligomers (and possibly other β-rich conformers) via the PrP_23–27 and PrP_90–110 segments, acting as Aβ receptor. On the other hand, PrP^Sc polymers efficiently bind to Aβ monomers and accelerate their oligomerization. To identify specific PrP sequences that are essential for the interaction between PrP polymers and Aβ peptide, we have co-expressed Aβ and PrP (or its shortened derivatives), fused to different fluorophores, in the yeast cell. Our data show that the 90–110 and 28–89 regions of PrP control the binding of proteinase-resistant PrP polymers to the Aβ peptide, whereas the 23–27 segment of PrP is dispensable for this interaction. This indicates that the set of PrP fragments involved in the interaction with Aβ depends on PrP conformational state.     

Identification of Markers for Newly Formed ��-Cells in the Perinatal Period: A Time of Recognized ��-Cell Immaturity

Markers of β-cell maturity would be useful in staging the differentiation of stem/progenitor cells to β-cells whether in vivo or in vitro. We previously identified markers for newly formed β-cells in regenerating rat pancreases after 90% partial pancreatectomy. To test the generality of these markers of newly formed β-cells, we examined their expression during the perinatal period, a time of recognized β-cell immaturity. We show by semiquantitative RT-PCR and immunostaining over the time course from embryonic day 18/20 to birth, 1 day, 2 days, 3 days, 7 days, and adult that MMP-2, CK-19, and SPD are truly markers of new and immature β-cells and that their expression transiently peaks in the perinatal period and is not entirely synchronous. The shared expression of these markers among fetal, newborn, and newly regenerated β-cells, but not adult, strongly supports their use as potential markers for new β-cells in the assessment of both the maturity of stem cell–derived insulin-producing cells and the presence of newly formed islets (neogenesis) in the adult pancreas. (J Histochem Cytochem 58:369–376, 2010)     

Quest for minor but key chlorophyll molecules in photosynthetic reaction centers – unusual pigment composition in the reaction centers of the chlorophyll d-dominated cyanobacterium Acaryochloris marina

A short overview, based on our own findings, is given of the minor pigments that function as key components in photosynthesis. Recently, we found the presence of chlorophyll a, chlorophyll d′ and pheophytin a as minor pigments in the chlorophyll d-dominated cyanobacterium Acaryochloris marina. This revised version was published online in June 2006 with corrections to the Cover Date.     

β-Mannanase (Man26A) and α-galactosidase (Aga27A) synergism – A key factor for the hydrolysis of galactomannan substrates

This study investigated the behavior of mannan-degrading enzymes, specifically focusing on differences with respect to their substrate specificities and their synergistic associations with enzymes from different glycoside hydrolase (GH) families. Galactosidases from Cyamopsis tetragonolobus seeds (Aga27A, GH27) and Aspergillus niger (AglC, GH36) were evaluated for their abilities to synergistically interact with mannanases from Clostridium cellulovorans (ManA, GH5) and A. niger (Man26A, GH26) in hydrolysis of guar gum and locust bean gum. Among the mannanases, Man26A was more efficient at hydrolyzing both galactomannan substrates, while among the galactosidases; Aga27A was the most effective at removing galactose substituents on both galactomannan substrates and galactose-containing oligosaccharides. An optimal protein mass ratio of glycoside hydrolases required to maximize the release of both reducing sugar and galactose residues was determined. Clear synergistic enhancement of locust bean gum hydrolysis with respect to reducing sugar release was observed when both mannanases at 75% enzyme dosage were supplemented with 25% enzyme protein dosage of Aga27A. At a protein ratio of 75% Man26A to 25% Aga27A, the presence of Man26A significantly enhanced galactose release by 25% Aga27A (2.36 fold) with locust bean gum, compared to when Aga27A was used alone at 100% enzyme protein dosage. A dosage of Aga27A at 75% and ManA at 25% protein content liberated the highest reducing sugar release on guar gum hydrolysis. A dosage of Man26A and Aga27A at 75–25% protein content, respectively, liberated reducing sugar release equivalent to that when Man26A was used alone at 100% protein content. From the findings obtained in this study, it was observed that the GH family classification of an enzyme affects its substrate specificity and synergistic interactions with other glycoside hydrolases from different families (more so than its EC classification). The GH26 Man26A and GH27 Aga27A enzymes appeared to be more promising for applications that involve the hydrolysis of galactomannan containing biomass. This method of screening for maximal compatibility between various GH families can ultimately lead to a more rational development of tailored enzyme cocktails for lignocellulose hydrolysis.     

A raison d'être for two distinct pathways in the early steps of plant isoprenoid biosynthesis?

When compared to other organisms, plants are atypical with respect to isoprenoid biosynthesis: they utilize two distinct and separately compartmentalized pathways to build up isoprene units. The co-existence of these pathways in the cytosol and in plastids might permit the synthesis of many vital compounds, being essential for a sessile organism. While substrate exchange across membranes has been shown for a variety of plant species, lack of complementation of strong phenotypes, resulting from inactivation of either the cytosolic pathway (growth and development defects) or the plastidial pathway (pigment bleaching), seems to be surprising at first sight. Hundreds of isoprenoids have been analyzed to determine their biosynthetic origins. It can be concluded that in angiosperms, under standard growth conditions, C??-phytyl moieties, C??-triterpenes and C??-carotenoids are made nearly exclusively within compartmentalized pathways, while mixed origins are widespread for other types of isoprenoid-derived molecules. It seems likely that this coexistence is essential for the interaction of plants with their environment. A major purpose of this review is to summarize such observations, especially within an ecological and functional context and with some emphasis on regulation. This latter aspect still requires more work and present conclusions are preliminary, although some general features seem to exist.     

Drosophila pupal macrophages – A versatile tool for combined ex vivo and in vivo imaging of actin dynamics at high resolution

Molecular understanding of actin dynamics requires a genetically traceable model system that allows live cell imaging together with high-resolution microscopy techniques. Here, we used Drosophila pupal macrophages that combine many advantages of cultured cells with a genetic in vivo model system. Using structured illumination microscopy together with advanced spinning disk confocal microscopy we show that these cells provide a powerful system for single gene analysis. It allows forward genetic screens to characterize the regulatory network controlling cell shape and directed cell migration in a physiological context. We knocked down components regulating lamellipodia formation, including WAVE, single subunits of Arp2/3 complex and CPA, one of the two capping protein subunits and demonstrate the advantages of this model system by imaging mutant macrophages ex vivo as well as in vivo upon laser-induced wounding.