ALBERT

Beschreibung: Previous work has demonstrated that phorbol ester (TPA)-induced adherence of human U937 myeloid leukemia cells can be blocked upon down-modulation of the beta-2-integrin CD11b after stable transfection of U937 cells with a pMTH1 vector-containing the CD11b gene in antisense orientation (asCD11b-U937) [Otte et al., (2011)]. In the present study, alterations in metabolism-associated factors, particularly intra- and extracellular proteases were investigated. A measurement of telomerase activity in the leukemic cells revealed continuously decreasing telomere adducts within 72h of TPA treatment in pMTH1-U937 cells. In contrast, telomerase activity sustained in asCD11b-U937 upon TPA-induced differentiation. Flow cytometric analysis confirmed unchanged CD11b levels in TPA-induced asCD11b-U937 in contrast to elevated levels in pMTH1-U937 whereby the expression of other beta-2-integrins including CD11a, CD11c and CD18 was increased in both populations after TPA treatment. Moreover, adherent pMTH1-U937 demonstrated the expression of monocytic differentiation markers including F4-80 and CD14 and an increased MIP-1-alpha production which remained at low or undetectable in TPA-induced asCD11b-U937. These effects indicated an altered response of the different cell populations to the TPA-induced differentiation process. Indeed, Western blot analysis revealed differences in the expression levels of intracellular metabolic factors including MnSOD and p97/VCP and after measurement of 20S proteasomal proteolytic activity. In addition, increased levels of extracellular metabolic factors including the matrix metalloproteinases MMP-1, MMP-7 and MMP-9 were observed in pMTH1-U937 cells in contrast to unaltered levels in asCD11b-U937 cells.

Beschreibung: Background Protein phosphorylation is responsible for a large portion of the regulatory functions of eukaryotic cells. Although the list of sequenced genomes of filamentous fungi has grown rapidly, the kinomes of recently sequenced species have not yet been studied in detail. The objective of this study is to apply a comparative analysis of the kinase distribution in different fungal phyla, and to explore its relevance to understanding the evolution of fungi and their taxonomic classification. We have analyzed in detail 12 subgroups of kinases and their distribution over 30 species, as well as their potential use as a classifier for members of the fungal kingdom. Results Our findings show that despite the similarity of the kinase distribution in all fungi, their domain distributions and kinome density can potentially be used to classify them and give insight into their evolutionary origin. In general, we found that the overall representation of kinase groups is similar across fungal genomes, the only exception being a large number of tyrosine kinase-like (TKL) kinases predicted in Laccaria bicolor. This unexpected finding underscores the need to continue to sequence fungal genomes, since many species or lineage-specific properties may remain to be discovered. Furthermore, we found that the domain organization significantly varies between the fungal species. Our results suggest that protein kinases and their functional domains strongly reflect fungal taxonomy. Conclusions Comparison of the predicted kinomes of sequenced fungi suggests essential signaling functions common to all species, but also specific adaptations of the signal transduction networks to particular species.

Beschreibung: Background A gene-regulatory network (GRN) refers to DNA segments that interact through their RNA and protein products and thereby govern the rates at which genes are transcribed. Creating accurate dynamic models of GRNs is gaining importance in biomedical research and development. To improve our understanding of continuous deterministic modeling methods employed to construct dynamic GRN models, we have carried out a comprehensive comparative study of three commonly used systems of ordinary differential equations: The S-system (SS), artificial neural networks (ANNs), and the general rate law of transcription (GRLOT) method. These were thoroughly evaluated in terms of their ability to replicate the reference models' regulatory structure and dynamic gene expression behavior under varying conditions. Results While the ANN and GRLOT methods appeared to produce robust models even when the model parameters deviated considerably from those of the reference models, SS-based models exhibited a notable loss of performance even when the parameters of the reverse-engineered models corresponded closely to those of the reference models: this is due to the high number of power terms in the SS-method, and the manner in which they are combined. In cross-method reverse-engineering experiments the different characteristics, biases and idiosynchracies of the methods were revealed. Based on limited training data, with only one experimental condition, all methods produced dynamic models that were able to reproduce the training data accurately. However, an accurate reproduction of regulatory network features was only possible with training data originating from multiple experiments under varying conditions. Conclusions The studied GRN modeling methods produced dynamic GRN models exhibiting marked differences in their ability to replicate the reference models' structure and behavior. Our results suggest that care should be taking when a method is chosen for a particular application. In particular, reliance on only a single method might unduly bias the results.

Beschreibung: Previous work has demonstrated that phorbol ester (TPA)-induced adherence of human U937 myeloid leukemia cells can be blocked upon down-modulation of the β2-integrin CD11b after stable transfection of U937 cells with a pMTH1 vector-containing the CD11b gene in antisense orientation (asCD11b-U937) [Otte et al., (2011)]. In the present study, alterations in metabolism-associated factors, particularly intra- and extracellular proteases were investigated. A measurement of telomerase activity in the leukemic cells revealed continuously decreasing telomere adducts within 72 h of TPA treatment in pMTH1-U937 cells. In contrast, telomerase activity sustained in asCD11b-U937 upon TPA-induced differentiation. Flow cytometric analysis confirmed unchanged CD11b levels in TPA-induced asCD11b-U937 in contrast to elevated levels in pMTH1-U937 whereby the expression of other β2-integrins including CD11a, CD11c and CD18 was increased in both populations after TPA treatment. Moreover, adherent pMTH1-U937 demonstrated the expression of monocytic differentiation markers including F4-80 and CD14 and an increased MIP-1α production which remained at low or undetectable in TPA-induced asCD11b-U937. These effects indicated an altered response of the different cell populations to the TPA-induced differentiation process. Indeed, Western blot analysis revealed differences in the expression levels of intracellular metabolic factors including MnSOD and p97/VCP and after measurement of 20 S proteasomal proteolytic activity. In addition, increased levels of extracellular metabolic factors including the matrix metalloproteinases MMP-1, MMP-7 and MMP-9 were observed in pMTH1-U937 cells in contrast to unaltered levels in asCD11b-U937 cells.

Beschreibung: Background Hereditary Hemorrhagic Telangiectasia (HHT) is an autosomal dominant disease with a varying range of phenotypes involving abnormal vasculature primarily manifested as arteriovenous malformations in various organs, including the nose, brain, liver, and lungs. The varied presentation and involvement of different organ systems makes the choice of potential treatment medications difficult. Results A patient with a mixed-clinical presentation and presumed diagnosis of HHT, severe exertional dyspnea, and diffuse pulmonary shunting at the microscopic level presented for treatment. We sought to analyze her metabolomic plasma profile to assist with pharmacologic treatment selection. Fasting serum samples from 5 individuals (4 healthy and 1 with HHT) were metabolomically profiled. A global metabolic network reconstruction, Recon 1, was used to help guide the choice of medication via analysis of the differential metabolism between the patient and healthy controls using metabolomic data. Flux Balance Analysis highlighted changes in metabolic pathway activity, notably in nitric oxide synthase (NOS), which suggested a potential link between changes in vascular endothelial function and metabolism. This finding supported the use of an already approved medication, bevacizumab (Avastin). Following 2 months of treatment, the patient's metabolic profile shifted, becoming more similar to the control subject profiles, suggesting that the treatment was addressing at least part of the pathophysiological state. Conclusions In this 'individualized case study' of personalized medicine, we carry out untargeted metabolomic profiling of a patient and healthy controls. Rather than filtering the data down to a single value, these data are analyzed in the context of a network model of metabolism, in order to simulate the biochemical phenotypic differences between healthy and disease states; the results then guide the therapy. This presents one approach to achieving the goals of individualized medicine through Systems Biology and causal models analysis.

Beschreibung: Phorbol ester (TPA) treatment of human U937 myeloid leukemia cells is associated with increasing adherence and monocyte-like maturation whereby the role of β2 integrin-mediated attachment for subsequent growth properties and the differentiation program remains unclear. Here, stably-transfected U937 cells with a pMTH1 vector containing the β2 integrin gene of CD11b in antisense orientation (asCD11b-U937) demonstrated a significantly reduced proliferative capacity in contrast to control vector transfectants (pMTH1-U937) or wild-type U937 cells. Phorbol ester exposure induced adherence and growth arrest in more than 90% of pMTH1-U937 and wild-type U937 cells after 72 h. In contrast, TPA-treated asCD11b-U937 failed to attach and the proliferation continued in more than 30% of the cells. Moreover, increased apoptosis appeared in asCD11b-U937 after TPA induction in contrast to pMTH1-U937 cells. In addition, non-specific inhibition of adherence on an agarose surface demonstrated internucleosomal DNA fragmentation in both, pMTH1-U937 and asCD11b-U937 after TPA treatment indicating a functional relationship between abolished adherence, regulation of proliferation and induction of apoptosis. Western blot analysis revealed differences in the expression levels and altered phosphorylation patterns of Pyk-2, pp60src and p42/p44 MAP kinases between pMTH1-U937 and asCD11b-U937 following TPA exposure which was also substantiated by Pyk-2 immunoprecipitation. These findings suggested that induced adherence predominantly mediated by a functional CD11b/CD18 integrin in U937 cells is involved in the activation of downstream signaling kinases and contributes to cell cycle regulation and apoptosis during monocytic maturation.

Beschreibung: Background Animal African trypanosomiasis, sleeping sickness in humans and Nagana in cattle, is a resurgent disease in Africa caused by Trypanosoma parasites. Trans-sialidases expressed by trypanosomes play an important role in the infection cycle of insects and mammals. Whereas trans-sialidases of other trypanosomes like the American T. cruzi are well investigated, relatively little research has been done on these enzymes of T. congolense. Results Based on a partial sequence and an open reading frame in the WTSI database, DNA sequences encoding for eleven T. congolense trans-sialidase 1 variants with 96.3% overall amino acid identity were amplified. Trans-sialidase 1 variants were expressed as recombinant proteins, isolated and assayed for trans-sialylation activity. The purified proteins produced α2,3-sialyllactose from lactose by desialylating fetuin, clearly demonstrating their trans-sialidase activity. Using an HPLC-based assay, substrate specificities and kinetic parameters of two variants were characterized in detail indicating differences in substrate specificities for lactose, fetuin and synthetic substrates. Both enzymes were able to sialylate asialofetuin to an extent, which was sufficient to reconstitute binding sites for Siglec-4. A mass spectrometric analysis of the sialylation pattern of glycopeptides from fetuin revealed clear but generally similar changes in the sialylation pattern of the N-glycans on fetuin catalyzed by the trans-sialidases investigated. Conclusions The identification and characterization of a trans-sialidase gene family of the African parasite T. congolense has opened new perspectives for investigating the biological role of these enzymes in Nagana and sleeping sickness. Based on this study it will be interesting to address the expression pattern of these genes and their activities in the different stages of the parasite in its infection cycle. Furthermore, these trans-sialidases have the biotechnological potential to be used for enzymatic modification of sialylated glycoconjugates.