Computational models for inferring biochemical networks

Biochemical networks are of great practical importance. The interaction of biological compounds in cells has been enforced to a proper understanding by the numerous bioinformatics projects, which contributed to a vast amount of biological information. The construction of biochemical systems (systems of chemical reactions), which include both topology and kinetic constants of the chemical reactions, is NP-hard and is a well-studied system biology problem. In this paper, we propose a hybrid architecture, which combines genetic programming and simulated annealing in order to generate and optimize both the topology (the network) and the reaction rates of a biochemical system. Simulations and analysis of an artificial model and three real models (two models and the noisy version of one of them) show promising results for the proposed method.The Romanian National Authority for Scientific Research, CNDI–UEFISCDI, Project No. PN-II-PT-PCCA-2011-3.2-0917

Hfe Deficiency Impairs Pulmonary Neutrophil Recruitment in Response to Inflammation

Regulation of iron homeostasis and the inflammatory response are tightly linked to protect the host from infection. Here we investigate how imbalanced systemic iron homeostasis in a murine disease model of hereditary hemochromatosis (Hfe−/− mice) affects the inflammatory responses of the lung. We induced acute pulmonary inflammation in Hfe−/− and wild-type mice by intratracheal instillation of 20 µg of lipopolysaccharide (LPS) and analyzed local and systemic inflammatory responses and iron-related parameters. We show that in Hfe−/− mice neutrophil recruitment to the bronchoalveolar space is attenuated compared to wild-type mice although circulating neutrophil numbers in the bloodstream were elevated to similar levels in Hfe−/− and wild-type mice. The underlying molecular mechanisms are likely multifactorial and include elevated systemic iron levels, alveolar macrophage iron deficiency and/or hitherto unexplored functions of Hfe in resident pulmonary cell types. As a consequence, pulmonary cytokine expression is out of balance and neutrophils fail to be recruited efficiently to the bronchoalveolar compartment, a process required to protect the host from infections. In conclusion, our findings suggest a novel role for Hfe and/or imbalanced iron homeostasis in the regulation of the inflammatory response in the lung and hereditary hemochromatosis

Functional analysis of Ig-α signaling in the context of B cell development and response

The B cell antigen receptor (BCR) signaling cascade is initiated by phosphorylation of tyrosine residues in the Immunoreceptor Tyrosine based Activation Motif (ITAM) of Ig-α and Ig-β. Signals initiated by the pre-BCR in pre-B cells and the BCR in immature and mature cells can lead to cell maturation, selection, terminal differentiation or cell death. It is still unclear how a single receptor can mediate such a variety of cellular responses. Our aim is to develop a system for the structural and functional analysis of Ig-α in vivo and to understand its role in B cell development, selection and response. We use retroviral gene transfer to introduce different mb-1 (Ig-α encoding gene) mutants into hematopoietic stem cells of Ig-α-deficient mice. Transduced cells are reinjected into irradiated recipient mice where they can differentiate into B cells. Here we have focused on the serine and threonine residues of the cytoplasmic region of Ig-α. These residues are phosphorylated upon BCR engagement and studies in cell lines indicated their potential negative regulatory role in BCR signaling. We found that Ig-α deficient hematopoietic stem cells transduced with retroviral vectors containing either the wild-type or a serine/threonine mutated mb-1 sequence were able to differentiate into IgM expressing cells in vivo. Thus, our data indicate that the serine and threonine residues do not play a dominant role in pre-BCR signaling as pre-B cells and immature B cells expressing serine and treonine mutant Ig-α develop. We are in the process of testing the effect of these mutations in B cell negative selection and B cell response

Protein tyrosine phosphatase 1B participates in the down-regulation of erythropoietin receptor signalling

Erythropoietin (EPO) is the principal hormone regulating the proliferation of erythroid precursors and their differentiation into erythrocytes. Binding of ligand to the cell-surface EPO-R (EPO receptor) induces dimerization and JAK2 (Janus kinase 2)-mediated tyrosine phosphorylation of the receptor. Less than 1% of the EPO-Rs are displayed on the cell surface; most of the receptor molecules are retained in intracellular compartments, including the ER (endoplasmic reticulum). Using pervanadate (PV) as a potent tool to inhibit cellular PTPs (protein tyrosine phosphatases), we demonstrated previously the accumulation of mature (endoglycosidase H-resistant) tyrosine-phosphorylated EPO-R [Cohen, Altaratz, Zick, Klingmuller and Neumann (1997) Biochem. J. 327, 391-397]. In the present study, we investigated the participation of the ER-associated PTP1B in the dephosphorylation of intracellular EPO-R. We demonstrate tyrosine phosphorylation of EPO-R in BOSC-23T cells co-expressing EPO-R and the 'substrate-trapping' mutant form of PTP1B, PTP1B D181A (referred to as PTP1BD). In vivo interaction between EPO-R and PTP1B suggested that PTP1B dephosphorylates the EPO-R intracellularly. Endoglycosidase H resistance of tyrosine-phosphorylated EPO-R in cells expressing PTP1BD suggested that mature EPO-R is dephosphorylated by PTP1B. Stimulation with EPO of cells co-expressing EPO-R and either PTP1BD or PTP1B resulted in an increase or decrease respectively in phosphotyrosine EPO-R. We thus suggest that PTP1B dephosphorylates EPO-stimulated EPO-R and participates in the down-regulation cascade of EPO-mediated signal transduction

pp\u2032DDE contamination of the blood and diet in central European populations

In this study, the actual risk of DDT pollution to two European human populations was assessed by analysing DDT residues in the diet, which is the main route of pollution for man, and in the blood and placenta, which are components affecting organs and new generations, respectively. The Gdansk region was selected as representative of areas subjected to a recent DDT ban in Europe, while a rural area in Western Germany was considered representative of European regions where DDT use and production ceased many years ago. The results of three food series of food sampling carried out with market basket methods during 2003 showed that pp'DDE, which is by far the main constituent of DDT residues, was present in foods of animal origin and in cereals at rather high concentrations in both countries, and that a risk for human health cannot be excluded. The total daily intake was higher in Poland than in Germany, and agrees with the finding that body tissues, on the average, are more polluted in donors from Poland than those from Germany

pp\u2019DDE contamination of blood and diet in central European populations

In this study, the actual risk of DDT pollution to two European human populations was assessed by analysing DDT residues in the diet, which is the main route of pollution for man, and in the blood and placenta, which are components affecting organs and new generations, respectively. The Gda\u144sk region was selected as representative of areas subjected to a recent DDT ban in Europe, while a rural area in Western Germany was considered representative of European regions where DDT use and production ceased many years ago. The results of three food series of food sampling carried out with market basket methods during 2003 showed that pp\u2032DDE, which is by far the main constituent of DDT residues, was present in foods of animal origin and in cereals at rather high concentrations in both countries, and that a risk for human health cannot be excluded. The total daily intake was higher in Poland than in Germany, and agrees with the finding that body tissues, on the average, are more polluted in donors from Poland than those from Germany

AURKA, DLGAP5, TPX2, KIF11 and CKAP5: Five specific mitosis-associated genes correlate with poor prognosis for non-small cell lung cancer patients

The growth of a tumor depends to a certain extent on an increase in mitotic events. Key steps during mitosis are the regulated assembly of the spindle apparatus and the separation of the sister chromatids. The microtubule-associated protein Aurora kinase A phosphorylates DLGAP5 in order to correctly segregate the chromatids. Its activity and recruitment to the spindle apparatus is regulated by TPX2. KIF11 and CKAP5 control the correct arrangement of the microtubules and prevent their degradation. In the present study, we investigated the role of these five molecules in non-small cell lung cancer (NSCLC). We analyzed the expression of the five genes in a large cohort of NSCLC patients (n=362) by quantitative real-time PCR. Each of the genes was highly overexpressed in the tumor tissues compared to corresponding normal lung tissue. The correlation of the expression of the individual genes depended on the histology. An increased expression of AURKA, DLGAP5, TPX2, KIF11 and CKAP5 was associated with poor overall survival (P=0.001-0.065). AURKA was a significant prognostic marker using multivariate analyses (P=0.006). Immunofluorescence studies demonstrated that the five mitosis-associated proteins co-localized with the spindle apparatus during cell division. Taken together, our data demonstrate that the expression of the mitosis-associated genes AURKA, DLGAP5, TPX2, KIF11 and CKAP5 is associated with the prognosis of NSCLC patients

Circulating neutrophil levels (in cells/nL) in wild-type and Hfe^−/− mice.

<p>Blood was obtained 4 h after intratracheal instillation of vehicle or 20 µg LPS. (A) Female wild-type and <i>Hfe^−/−</i> mice. n = 5–7 per group. ^‡<i>P</i><0.05 and ^★<i>P</i><0.001 versus WT control mice; ^†<i>P</i><0.05 versus <i>Hfe^−/−</i> control mice. (B) Male wild-type and <i>Hfe^−/−</i> mice. n = 9–11 per group. ^★<i>P</i><0.001 versus WT control mice; ^†<i>P</i><0.001 versus <i>Hfe^−/−</i> control mice.</p

Frequency of AIP Gene Mutations in Young Patients With Acromegaly: A Registry-Based Study

Context: Familial and sporadic GH-secreting pituitary adenomas are associated with mutations in the aryl hydrocarbon receptor-interacting protein (AIP) gene. Patients with an AIP mutation (AIPmut) tend to have more aggressive tumors occurring at a younger age. Objective: The objective of the study was to investigate the frequency of AIPmut in patients diagnosed at 30 years of age or younger. Design: The German Acromegaly Registry database (1795 patients in 58 centers) was screened for patients diagnosed with acromegaly at 30 years of age or younger (329 patients). Sixteen centers participated and 91 patients consented to AIPmut analysis. Intervention: DNA was analyzed by direct sequencing and multiplex ligation dependent probe amplification Main outcome Measures: The number of patients with AIPmut was measured. Results: Five patients had either a mutation (c.490C>T, c.844C>T, and c.911G>A, three males) or gross deletions of exons 1 and 2 of the AIP gene (n = 2, one female). The overall frequency of an AIPmut was 5.5%, and 2.3% or 2.4% in patients with an apparently sporadic adenoma or macroadenoma, respectively. By contrast, three of four patients (75%) with a positive family history were tested positive for an AIPmut. Except for a positive family history, there were no significant differences between patients with and without an AIPmut. Conclusions: The frequency of AIPmut in this registry-based cohort of young patients with acromegaly is lower than previously reported. Patients with a positive family history should be tested for an AIPmut, whereas young patients without an apparent family history should be screened, depending on the individual cost to benefit ratio