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Background: The optimization of metabolic rates (as linear objective functions) represents the methodical core of flux-balance analysis techniques which have become a standard tool for the study of genome-scale metabolic models. Besides (growth and synthesis) rates, metabolic yields are key parameters for the characterization of biochemical transformation processes, especially in the context of biotechnological applications. However, yields are ratios of rates, and hence the optimization of yields (as nonlinear objective functions) under arbitrary linear constraints is not possible with current flux-balance analysis techniques. Despite the fundamental importance of yields in constraint-based modeling, a comprehensive mathematical framework for yield optimization is still missing. Results: We present a mathematical theory that allows one to systematically compute and analyze yield-optimal solutions of metabolic models under arbitrary linear constraints . In particular, we formulate yield optimization as a linear-fractional program. For practical computations, we transform the linear-fractional yield optimization problem to a (higher-dimensional) linear problem. Its solutions determine the solutions of the original problem and can be used to predict yield-optimal flux distributions in genome-scale metabolic models. For the theoretical analysis, we consider the linear-fractional problem directly. Most importantly, we show that the yield-optimal solution set (like the rate-optimal solution set) is determined by (yield-optimal) elementary flux vectors of the underlying metabolic model. However, yield- and rate-optimal solutions may differ from each other, and hence optimal (biomass or product) yields are not necessarily obtained at solutions with optimal (growth or synthesis) rates. Moreover, we discuss phase planes/production envelopes and yield spaces, in particular, we prove that yield spaces are convex and provide algorithms for their computation. We illustrate our findings by a small example and demonstrate their relevance for metabolic engineering with realistic models of E. coli . Conclusions: We develop a comprehensive mathematical framework for yield optimization in metabolic models. Our theory is particularly useful for the study and rational modification of cell factories designed under given yield and/or rate requirements. [ABSTRACT FROM AUTHOR]

Abstract: The survival and proliferation of cells and organisms require a highly coordinated allocation of cellular resources to ensure the efficient synthesis of cellular components. In particular, the total enzymatic capacity for cellular metabolism is limited by finite resources that are shared between all enzymes, such as cytosolic space, energy expenditure for amino-acid synthesis, or micro-nutrients. While extensive work has been done to study constrained optimization problems based only on stoichiometric information, mathematical results that characterize the optimal flux in kinetic metabolic networks are still scarce. Here, we study constrained enzyme allocation problems with general kinetics, using the theory of oriented matroids. We give a rigorous proof for the fact that optimal solutions of the non-linear optimization problem are elementary flux modes. This finding has significant consequences for our understanding of optimality in metabolic networks as well as for the identification of metabolic switches and the computation of optimal flux distributions in kinetic metabolic networks. [Copyright &y& Elsevier]

Abstract: It is well known that representations of kernel-based approximants in terms of the standard basis of translated kernels are notoriously unstable. To come up with a more useful basis, we adopt the strategy known from Newton’s interpolation formula, using generalized divided differences and a recursively computable set of basis functions vanishing at increasingly many data points. The resulting basis turns out to be orthogonal in the Hilbert space in which the kernel is reproducing, and under certain assumptions it is complete and allows convergent expansions of functions into series of interpolants. Some numerical examples show that the Newton basis is much more stable than the standard basis of kernel translates. [Copyright &y& Elsevier]

We report on a comparative molecular cytogenetic and in silico study on evolutionary changes in human chromosome 7 homologs in all major primate lineages. The ancestral mammalian homologs comprise two chromosomes (7a and 7b/16p) and are conserved in carnivores. The subchromosomal organization of the ancestral primate segment 7a shared by a lemur and higher Old World monkeys is the result of a paracentric inversion. The ancestral higher primate chromosome form was then derived by a fission of 7b/16p, followed by a centric fusion of 7a/7b as observed in the orangutan. In hominoids two further inversions with four distinct breakpoints were described in detail: the pericentric inversion in the human/African ape ancestor and the paracentric inversion in the common ancestor of human and chimpanzee. FISH analysis employing BAC probes confined the 7p22.1 breakpoint of the pericentric inversion to 6.8 Mb on the human reference sequence map and the 7q22.1 breakpoint to 97.1 Mb. For the paracentric inversion the breakpoints were found in 7q11.23 between 76.1 and 76.3 Mb and in 7q22.1 at 101.9 Mb. All four breakpoints were flanked by large segmental duplications. Hybridization patterns of breakpoint-flanking BACs and the distribution of duplicons suggest their presence before the origin of both inversions. We propose a scenario by which segmental duplications may have been the cause rather than the result of these chromosome rearrangements. [Copyright &y& Elsevier]

FHL2 (Four and a Half LIM domain-containing protein 2) is a member of a small family of proteins with four LIM domains and an N-terminal half LIM domain. It is an intracellular protein thought to function as an adaptor in the formation of multi-protein complexes involved in signaling. To obtain human FHL2 in amounts allowing further characterization, we evaluated different expression systems and chose to express FHL2 with a His6 tag in insect cells using the baculovirus system. The recombinant protein was highly expressed and could be purified to >98% homogeneity as judged by SDS–PAGE analysis. Purified recombinant FHL2 was used to generate antibodies allowing detection and immunoprecipitation of FHL2 from human cells. Both recombinant and natural FHL2 were characterized by SDS–PAGE and MALDI-TOF mass spectrometry. The molecular mass of the recombinant His6-tagged protein obtained by mass spectrometry was 36,995 Da, in good agreement with the apparent mass of 36 kDa in SDS–PAGE and slightly higher than the 35,981 Da calculated from the sequence of the construct. The measured molecular mass of natural human FHL2 was 32,742 Da and the calculated mass was 32,192 Da. However, the apparent molecular mass in SDS–PAGE is 41 kDa, indicating that the natural protein has an abnormal electrophoretic mobility. The results show that both the recombinant and the natural proteins are post-translationally modified and indicate that such modifications may lead to an abnormal electrophoretic behavior of natural human FHL2. [Copyright &y& Elsevier]

Abstract Idiopathic pulmonary fibrosis (IPF) is a chronic fibrosing lung disease with a dismal prognosis and a largely unknown etiology. Autotaxin (ATX) is a secreted lysophospholipase D, largely responsible for extracellular production of lysophosphatidic acid (LPA), a bioactive phospholipid. LPA has numerous effects in most cell types, signaling through at least 6 receptors (LPAR) exhibiting wide spread distribution and overlapping specificities. The ATX/LPA axis has been suggested as a therapeutic target in different chronic inflammatory and fibroproliferative disorders, including pulmonary fibrosis. In this report, we examined head-to-head the efficacy of a potent inhibitor of ATX (PF-8380), that has not been tested in pulmonary fibrosis models, and an antagonist of LPAR1 (AM095) in bleomycin (BLM)-induced pulmonary fibrosis. Both compounds abrogated the development of pulmonary fibrosis and prevented the distortion of lung architecture, exhibiting qualitative and quantitative differences in different manifestations of the modeled disease. [ABSTRACT FROM AUTHOR]

Abstract: Let a family of gradient Gaussian vector fields on be given. We show the existence of a uniform finite range decomposition of the corresponding covariance operators, that is, the covariance operator can be written as a sum of covariance operators whose kernels are supported within cubes of diameters . In addition we prove natural regularity for the subcovariance operators and we obtain regularity bounds as we vary within the given family of gradient Gaussian measures. [Copyright &y& Elsevier]

Abstract: We estimate the rate of convergence of products of projections on K intersecting lines in . More generally, consider the orbit of a point under any sequence of orthogonal projections on K arbitrary lines in . Assume that the sum of the squares of the distances of the consecutive iterates is less than ε. We show that if ε tends to zero, then the diameter of the orbit tends to zero uniformly for all families of a fixed number K of lines. We relate this result to questions concerning convergence of products of projections on finite families of closed subspaces of . [Copyright &y& Elsevier]

Abstract: An Evolutionary Neo-Centromere (ENC) is a centromere that emerged in an ectopic region of a chromosome during evolution. It is thought that the old centromere must be inactivated because dicentric chromosomes are not viable. The aim of the present study was to investigate whether 3D arrangement in the interphase nucleus of the novel and old centromeric domains was affected by the repositioning event. The data we present here strongly indicate that the ENC phenomenon does not affect the 3D location of either novel or old centromeres. Very likely, other features, such as gene density, rather than the newly acquired or lost functions, define positioning in the nucleus. [Copyright &y& Elsevier]

Highlights: [•] microRNAs are silenced by histone acetylation. [•] 5-Aza-2′dC and SAHA induce microRNA re-expression. [•] 5-Aza-2′dC and SAHA are most efficient in combination. [ABSTRACT FROM AUTHOR]

Abstract: Background: We investigated the role of the programmed cell death 4 (PDCD4) tumor suppressor gene in specimens of transitional cell carcinoma and of healthy individuals. Methods: PDCD4 immunohistochemical expression was investigated in 294 cases in histologically proven transitional cell carcinoma in different tumorous stages (28 controls, 122 non-muscle invasive urothelial carcinoma, stages Tis-T1, 119 invasive transitional cell carcinoma stages T2–T4 and 25 metastases). MiR-21 expression, an important PDCD4 regulator, was assessed with real-time PCR analysis and showed inverse correlation to tissue PDCD4 expression. Results: Nuclear and cytoplasmatic PDCD4 immunostaining decreased significantly with histopathological progression of the tumor (p <0001). Controls showed strong nuclear and cytoplasmatic immunohistochemical staining. MiR-21 up regulation in tissue corresponded to PDCD4 suppression. Conclusions: These data support a decisive role for PDCD4 down regulation in transitional cell carcinoma and confirm miR-21 as a negative regulator for PDCD4. Additionally, PDCD4 immunohistochemical staining turns out to be a possible diagnostic marker for transitional cell carcinoma. [Copyright &y& Elsevier]

Abstract: Gene silencing by epigenetic mechanisms is frequent in prostate cancer (PCA). The link between DNA hypermethylation and histone modifications is not completely understood. We chose the GSTP1 gene which is silenced by hypermethylation to analyze the effect of the histone deacetylase inhibitor depsipeptide on DNA methylation and histone modifications at the GSTP1 promoter site. Prostate cell lines (PC-3, LNCaP, and BPH-1) were treated with depsipeptide; apoptosis (FACS analysis), GSTP1 mRNA levels (quantitative real-time PCR), DNA hypermethylation (methylation-specific PCR), and histone modifications (chromatin immunoprecipitation) were studied. Depsipeptide induced apoptosis in PCA cells, but not a cell cycle arrest. Depispeptide reversed DNA hypermethylation and repressive histone modifications (reduction of H3K9me2/3 and H3K27me2/3; increase of H3K18Ac), thereby inducing GSTP1 mRNA re-expression. Successful therapy requires both, DNA demethylation and activating histone modifications, to induce complete gene expression of epigenetically silenced genes and depsipeptide fulfils both criteria. [Copyright &y& Elsevier]

In this study the UV-attenuating properties of microparticles consisting of a benzotriazole derivative were investigated, which are used as absorbers for UV radiation in cosmetic sunscreens. The particles were micronized in presence of a dispersing agent by means of a ball milling process. According to the energy input different particle sizes were produced in the range of 0.16 to 4 μm. In order to study even smaller particles, the sample with particle size 0.16 μm was fractionated further by centrifugation. Particle sizes were measured using fiberoptic quasi-elastic light scattering (FOQELS) and laser diffractometry. The UV-attenuating properties of the dispersions with different particle sizes were assessed using UV spectroscopy. With decreasing particle size the efficiency of the UV extinction of the dispersion increases up to a particle size of 80 nm. For particles smaller than 80 nm the UV extinction decreases again indicating an optimum at 80 nm. From reflection spectroscopic measurements it was found that scattering makes about 10%, and absorption 90%, of the UV-attenuating effect of the particles, which are obtained at the end of the milling process. [Copyright &y& Elsevier]

Mutations in the SALL1 gene on chromosome 16q12.1 cause Townes–Brocks syndrome (TBS). This autosomal dominantly inherited disorder is characterized by typical malformations of the thumbs, the ears, and the anus, and also commonly affects the kidneys and other organ systems. SALL1 has recently been shown to localize to chromocenters and other heterochromatin foci in murine fibroblasts and to interact with the telomere-repeat-binding factor TRF1/PIN2. Here, we show that the ubiquitin-conjugating enzyme 2I (UBE2I), the human homolog of S. cerevisiae UBC9, and the small ubiquitin-like modifier-1 (SUMO-1) interact with SALL1 in the yeast two-hybrid system. The interaction of SALL1 and UBE2I was confirmed in a glutathione S-transferase (GST) pull-down experiment. In an in vitro assay, it could be demonstrated that SALL1 is covalently modified by at least two SUMO-1 molecules in the presence of UBA2/AOS1 and UBE2I. Mutation of lysine 1086 of SALL1 to arginine abrogates SALL1 sumoylation, suggesting the presence of a polymeric SUMO-1 chain in the wild type state. [Copyright &y& Elsevier]