Simplified absolute metabolite quantification by gas chromatography-isotope dilution mass spectrometry on the basis of commercially available source material

In the field of metabolomics, GC-MS has rather established itself as a tool for semi-quantitative strategies like metabolic fingerprinting or metabolic profiling. Absolute quantification of intra- or extracellular metabolites is nowadays mostly accomplished by application of diverse LC-MS techniques. Only few groups have so far adopted GC-MS technology for this exceptionally challenging task. Besides numerous and deeply investigated problems related to sample generation, the pronounced matrix effects in biological samples have led to the almost mandatory application of isotope dilution mass spectrometry (IDMS) for the accurate determination of absolute metabolite concentrations. Nevertheless, access to stable isotope labeled internal standards (ILIS), which are in many cases commercially unavailable, is quite laborious and very expensive. Here we present an improved and simplified gas chromatography-isotope dilution mass spectrometry (GC-IDMS) protocol for the absolute determination of intra- and extracellular metabolite levels. Commercially available (13)C-labeled algal cells were used as a convenient source for the preparation of internal standards. Advantages as well as limitations of the described method are discussed.     

Thrombin induces Egr-1 expression in fibroblasts involving elevation of the intracellular Ca2+ concentration, phosphorylation of ERK and activation of ternary complex factor

Background

The Arthropods are a diverse group of organisms including Chelicerata (ticks, mites, spiders), Crustacea (crabs, shrimps), and Insecta (flies, mosquitoes, beetles, silkworm). The cattle tick, Rhipicephalus (Boophilus) microplus, is an economically significant ectoparasite of cattle affecting cattle industries world wide. With the availability of sequence reads from the first Chelicerate genome project (the Ixodes scapularis tick) and extensive R. microplus ESTs, we investigated evidence for putative RNAi proteins and studied RNA interference in tick cell cultures and adult female ticks targeting Drosophila homologues with known cell viability phenotype.

Results

We screened 13,643 R. microplus ESTs and I. scapularis genome reads to identify RNAi related proteins in ticks. Our analysis identified 31 RNAi proteins including a putative tick Dicer, RISC associated (Ago-2 and FMRp), RNA dependent RNA polymerase (EGO-1) and 23 homologues implicated in dsRNA uptake and processing. We selected 10 R. microplus ESTs with >80% similarity to D. melanogaster proteins associated with cell viability for RNAi functional screens in both BME26 R. microplus embryonic cells and female ticks in vivo. Only genes associated with proteasomes had an effect on cell viability in vitro. In vivo RNAi showed that 9 genes had significant effects either causing lethality or impairing egg laying.

Conclusion

We have identified key RNAi-related proteins in ticks and along with our loss-of-function studies support a functional RNAi pathway in R. microplus. Our preliminary studies indicate that tick RNAi pathways may differ from that of other Arthropods such as insects.     

Non-synonymous gene polymorphisms in the secretory signal peptide of human TGF-β1 affect cellular synthesis but not secretion of TGF-β1

We have demonstrated that gene polymorphisms within the N-terminal leader sequence of TGF-β1 contribute to the outcome of hepatic fibrogenesis. In addition, the polymorphism at codon 25 affects TGF-β1 production in peripheral blood leukocytes. Therefore, it is general assumed that these polymorphisms influence cellular secretion of this cytokine. In the present study, we analysed if this widespread hypothesis is true. We cloned FLAG-tagged CMV-driven human full-length TGF-β1 expression constructs of the different allelic variations (i.e. 10Leu/25Arg, 10Pro/25Pro and 10Pro/25Arg) and transfected them into the immortal hepatic stellate cell line LX-2 and Chinese Hamster Ovary cells. Surprisingly, the allelic variants carrying a proline either in codon 10 or 25 showed overall reduced expression as assessed by Western blot and quantitative ELISA. We conclude that the allelic variations within the signal sequence influence the expression and not secretion of TGF-β1. Detailed RNA structure prediction analysis further suggests that the individual variants form different secondary structures.     

Complement activation,regulation, and molecular basis for complement‐related diseases

The complement system is an essential element of the innate immune response that becomes activated upon recognition of molecular patterns associated with microorganisms, abnormal host cells, and modified molecules in the extracellular environment. The resulting proteolytic cascade tags the complement activator for elimination and elicits a pro‐inflammatory response leading to recruitment and activation of immune cells from both the innate and adaptive branches of the immune system. Through these activities, complement functions in the first line of defense against pathogens but also contributes significantly to the maintenance of homeostasis and prevention of autoimmunity. Activation of complement and the subsequent biological responses occur primarily in the extracellular environment. However, recent studies have demonstrated autocrine signaling by complement activation in intracellular vesicles, while the presence of a cytoplasmic receptor serves to detect complement‐opsonized intracellular pathogens. Furthermore, breakthroughs in both functional and structural studies now make it possible to describe many of the intricate molecular mechanisms underlying complement activation and the subsequent downstream events, as well as its cross talk with, for example, signaling pathways, the coagulation system, and adaptive immunity. We present an integrated and updated view of complement based on structural and functional data and describe the new roles attributed to complement. Finally, we discuss how the structural and mechanistic understanding of the complement system rationalizes the genetic defects conferring uncontrolled activation or other undesirable effects of complement.     

The modular habitat model (MHM) for the ide, Leuciscus idus (L.) - a new method to predict the suitability of inshore habitats for fish

Groynes are the dominant river engineering structures along the lowland section of large European rivers such as the Rhine, Danube and the Elbe. More than 6000 groynes structure the 400 km stretch of the potamal of the Elbe River. After 1945, destruction of the groynes increased through ice and flood events in the eastern part of Germany. In the past ten years, groyne reconstruction was accompanied by a controversial discussion in the context of the ecological integrity of the Elbe River. With the modular habitat model (MHM) a tool was developed to evaluate the suitability and to balance the availability of fish habitats in groyne fields of different conditions. The morphodynamic module produced a digital terrain model and a spatial model of flow velocity for each groyne field separately. Based on point abundance sampling by electro‐fishing, models of habitat preference were developed for different life history stages by logistic regression. Statistical models predicting the preference of fish‐environment relationships (Leuciscus idus) at different life history stages. The models were discriminated and validated by receiver operating characteristic (ROC) curves. The link between the statistical and the spatial model was realised in the suitability module. The suitability of microhabitats is expressed in classes for each species and life history stage separately. Habitat availability is balanced on the level of mesohabitat, e.g. different types of groyne fields. The temporal dynamics of habitat availability are analysed by considering different levels of discharge. For the stage ‘juvenile A’ and preadult the habitat suitability is better in fields downstream of destroyed groynes. For ‘juvenile B’ and adult stages of the ide, groyne fields in general constitute low habitat suitability. Differences in spatial availability are higher than the differences in temporal habitat availability.     

Cerebral vein thrombosis: clinical manifestation and diagnosis

Background  

Cerebral venous thrombosis (CVT) is a disease with a wide spectrum of symptoms and severity. In this study we analysed the predictive value of clinical signs and symptoms and the contribution of D-dimer measurements for diagnosis.     

Diplosegmentation in the pill millipede Glomeris marginata is the result of dorsal fusion

All trunk segments in the pill millipede Glomeris marginata (Myriapoda: Diplopoda) are initially patterned genetically, (as visualized by the embryonic expression pattern of the even‐skipped gene) and formed morphologically, (as visualized by 4‐6‐diamidin‐2‐phenylindol stained embryos) in a single segmental period. In addition, formation of every nascent trunk segment concerns ventral as well as dorsal segmental units. Only after the formation of the nascent posterior trunk segments, the dorsal segmental units of two adjacent segments fuse to form a single dorsal segmental unit that subsequently covers two ventral leg‐bearing segmental units. The formation of a diplosegmental unit, or in short a diplosegment, is thus the result of dorsal fusion of embryonic tissue and not the result of any splitting‐process or fusion of dorsal tergites. The new data also argue against heterochrony as a primary causative factor for the formation of the diplosegments during the formation of dorsal versus ventral segmental units. Furthermore, no evidence was found supporting the hypothesis that anterior trunk segments in diplopods represent degenerate diplosegments. Two possible scenarios arise from the ontogenetic data presented here, whether this represents an ancestral feature of the diplopods, or alternatively if they represent an isolated case only found in Glomeris (and close relatives). If the former is the case, my work may provide an impressive example of Haeckel's recapitulation theory.     

Quantification of Interaction Strengths between Chaperones and Tetratricopeptide Repeat Domain-containing Membrane Proteins

The three tetratricopeptide repeat domain-containing docking proteins Toc64, OM64, and AtTPR7 reside in the chloroplast, mitochondrion, and endoplasmic reticulum of Arabidopsis thaliana, respectively. They are suggested to act during post-translational protein import by association with chaperone-bound preprotein complexes. Here, we performed a detailed biochemical, biophysical, and computational analysis of the interaction between Toc64, OM64, and AtTPR7 and the five cytosolic chaperones HSP70.1, HSP90.1, HSP90.2, HSP90.3, and HSP90.4. We used surface plasmon resonance spectroscopy in combination with Interaction Map® analysis to distinguish between chaperone oligomerization and docking protein-chaperone interactions and to calculate binding affinities for all tested interactions. Complementary to this, we applied pulldown assays as well as microscale thermophoresis as surface immobilization independent techniques. The data revealed that OM64 prefers HSP70 over HSP90, whereas Toc64 binds all chaperones with comparable affinities. We could further show that AtTPR7 is able to bind HSP90 in addition to HSP70. Moreover, differences between the HSP90 isoforms were detected and revealed a weaker binding for HSP90.1 to AtTPR7 and OM64, showing that slight differences in the amino acid composition or structure of the chaperones influence binding to the tetratricopeptide repeat domain. The combinatory approach of several methods provided a powerful toolkit to determine binding affinities of similar interaction partners in a highly quantitative manner.