Hybrid elementary flux analysis/nonparametric modeling: application for bioprocess control

Background  

The progress in the "-omic" sciences has allowed a deeper knowledge on many biological systems with industrial interest. This knowledge is still rarely used for advanced bioprocess monitoring and control at the bioreactor level. In this work, a bioprocess control method is presented, which is designed on the basis of the metabolic network of the organism under consideration. The bioprocess dynamics are formulated using hybrid rigorous/data driven systems and its inherent structure is defined by the metabolism elementary modes.     

SIRAC: Supervised Identification of Regions of Aberration in aCGH datasets

Background  

Array comparative genome hybridization (aCGH) provides information about genomic aberrations. Alterations in the DNA copy number may cause the cell to malfunction, leading to cancer. Therefore, the identification of DNA amplifications or deletions across tumors may reveal key genes involved in cancer and improve our understanding of the underlying biological processes associated with the disease.     

The role of JNK pathway in familial Parkinson's disease

Parkinson's disease is a neurodegenerative disorder characterized by a dramatic loss of dopaminergic neurons in the substantia nigra. Among the many pathogenic mechanisms thought to contribute to the demise of these cells in sporadic cases of PD, oxidative stress has taken center stage due to extensive experimental evidence showing that dopamine- or MPTP-derived reactive oxygen species and oxidized dopamine metabolites may trigger toxicity through mitochondrial inhibition or deleterious modifications of biomolecules. In familial forms of PD, however, the involvement of toxic protein aggregation (synuclein), impairment of ubiquitin-proteosome system (parkin. and loss of antioxidative properties (DJ-1) has gained attention. Recently, JNK pathway has come to light that could link malfunction of mutated DJ-1, parkin, PINK1 and alpha-synuclein to the oxidative stress-triggered apoptosis, finally ascribing a common pathogenic mechanism to both the sporadic and familial forms of PD.     

Influence of subinhibitory concentrations of amikacin and ciprofloxacin on morphology and adherence ability of uropathogenic strains

The influence of subinhibitory concentrations (1/2, 1/4, 1/8, 1/16 and 1/32 MIC) of amikacin and ciprofloxacin on the morphology and adherence of uropathogenic strains was studied. Intensity of morphological changes was proportional to the concentrations of these antibiotics. Morphological changes were the most prominent after bacterial exposure to sub-MICs of ciprofloxacin. These concentrations, especially 1/2 MIC of ciprofloxacin, induced the formation of filaments of E. coli, K. pneumoniae, K. oxytoca, E. cloacae and A. calcoaceticus biotype anitratus. No morphological changes were observed in P. aeruginosa, S. epidermidis and S. aureus cells after exposure to subinhibitory concentrations of both antibiotics. Sub-MICs of amikacin affected the changes in cell shape only slightly. The exposure of bacterial strains to 1/2 MIC of ciprofloxacin induced increased vacuolation of the cells. We observed shrinkage of the protoplasm and the pleated cell walls in comparison with control cells. The greatest loss of adherence ability occurred at 1/2 MIC of ciprofloxacin after a 1-d incubation.     

Arginine vasopressin-mediated cardiac differentiation: insights into the role of its receptors and nitric oxide signaling

Despite the existence of a functional arginine vasopressin (AVP) system in the adult heart and evidence that AVP induces myogenesis, its significance in cardiomyogenesis is currently unknown. In the present study, we hypothesized a role for AVP in cardiac differentiation of D3 and lineage-specific embryonic stem (ES) cells expressing green fluorescent protein under the control of atrial natriuretic peptide (Anp) or myosin light chain-2V (Mlc-2V) promoters. Furthermore, we investigated the nitric oxide (NO) involvement in AVP-mediated pathways. AVP exposure increased the number of beating embryoid bodies, fluorescent cells, and expression of Gata-4 and other cardiac genes. V1a and V2 receptors (V1aR and V2R) differentially mediated these effects in transgenic ES cells, and exhibited a distinct developmentally regulated mRNA expression pattern. A NO synthase inhibitor, L-NAME, powerfully antagonized the AVP-induced effects on cardiogenic differentiation, implicating NO signaling in AVP-mediated pathways. Indeed, AVP elevated the mRNA and protein levels of endothelial NO synthase (eNOS) through V2R stimulation. Remarkably, increased beating activity was found in AVP-treated ES cells with down-regulated eNOS expression, indicating the significant involvement of additional pathways in cardiomyogenic effects of AVP. Finally, patch clamp recordings revealed specific AVP-induced changes of action potentials and increased L-type Ca2+ (ICa,L) current densities in differentiated ventricular phenotypes. Thus, AVP promotes cardiomyocyte differentiation of ES cells and involves Gata-4 and NO signaling. AVP-induced action potential prolongation appears likely to be linked to the increased ICa,L current in ventricular cells. In conclusion, this report provides new evidence for the essential role of the AVP system in ES cell-derived cardiomyogenesis.