Simulating brain tumor heterogeneity with a multiscale agent-based model: Linking molecular signatures,phenotypes and expansion rate

We have extended our previously developed 3D multi-scale agent-based brain tumor model to simulate cancer heterogeneity and to analyze its impact across the scales of interest. While our algorithm continues to employ an epidermal growth factor receptor (EGFR) gene–protein interaction network to determine the cells’ phenotype, it now adds an implicit treatment of tumor cell adhesion related to the model’s biochemical microenvironment. We simulate a simplified tumor progression pathway that leads to the emergence of five distinct glioma cell clones with different EGFR density and cell ‘search precisions’. The in silico results show that microscopic tumor heterogeneity can impact the tumor system’s multicellular growth patterns. Our findings further confirm that EGFR density results in the more aggressive clonal populations switching earlier from proliferation-dominated to a more migratory phenotype. Moreover, analyzing the dynamic molecular profile that triggers the phenotypic switch between proliferation and migration, our in silico oncogenomics data display spatial and temporal diversity in documenting the regional impact of tumorigenesis, and thus support the added value of multi-site and repeated assessments in vitro and in vivo. Potential implications from this in silico work for experimental and computational studies are discussed.     

Transillumination spatially modulated illumination microscopy

The diagnostic utility of a conventional transillumination microscope, the most common imaging modality in clinical use today, is limited by the microscope's resolution. It is, however, possible to achieve lateral resolution well beyond the classical limit by using laterally structured illumination in a wide-field, nonconfocal microscope. In this method, the spatially modulated illumination (SMI) makes high-resolution information that is normally inaccessible visible in the observed image. Previously presented SMI microscopy systems operated in epifluorescence mode. We describe the design, construction, and testing of a novel transillumination SMI microscope. As transillumination is necessary for most medical applications, such as histopathologic evaluation of biopsy tissue and chromosomal analysis, such a system should have a significant diagnostic effect.     

Liquid chromatographic profiles of individual compounds of technical toxaphene

The elution orders of 20 hexa- to nonachlorobornanes and five hexa- to octachlorocamphenes were studied with normal-phase silica and amino phase HPLC, reversed-phase HPLC, as well as gel-permeation chromatography (GPC). Twenty-one compounds of technical toxaphene (CTTs) are commercially available and four were isolated from environmental samples. Structure-activity relationships and chromatographic properties were deduced from the data sets derived on these LC systems. The retention on silica (low-resolution LC and HPLC) increased with the polarity of the CTTs. The elution order of CTTs on amino normal-phase HPLC was, for the most part, the same as on silica normal-phase HPLC. The degree of chlorination determined the elution order of CTTs on C18 RP-HPLC. CTTs eluted from medium-pressure GPC with decreasing molecular size. Chlorobornanes with dichloro substituents on the six-membered ring eluted after the chloroboranes without geminal chlorine atoms on secondary carbons, indicating that these congeners are larger. Altogether, the results increase the knowledge of complex substance class and may serve as a tool in order to gain further standard components.     

The performance of 1‐ethyl‐3‐methylimidazolium tetrafluoroborate ionic liquid as mobile phase additive in HPLC‐based lipophilicity assessment

Ionic liquids have been widely used as green alternative mobile phase additives to shield the residuals silanols groups and modify the stationary/mobile phase HPLC systems. The present study aimed to evaluate the performance of the ionic liquid 1‐ethyl‐3‐methylimidazolium tetrafluoroborate ([EMIM][BF4]) in producing extrapolated logk_w indices suitable to substitute for octanol–water logP or logD values. The effect of [EMIM][BF4] was investigated for a set of basic and neutral drugs using two different columns, BDS and ABZ⁺. [EMIM][BF4] was added simply alone or in combination with n‐octanol and was compared with the conventional masking agent n‐decylamine. [EMIM][BF4] reduced the retention by suppressing silanophilic interactions, althoug to a lower extent than n‐decylamine. Addition of n‐octanol further decreased the retention by shielding silanol sites on BDS and/or interacting with polar groups through hydrogen bonding on ABZ⁺. Logk_w/logD_7.4 relationships proved moderate compared with those derived upon addition of n‐decylamine. They were considerably improved upon the introduction of protonated fraction F⁺ in the correlation, reflecting ion pair formation between the chaotropic anion [BF4]^‐ and the protonated basic compounds. In this aspect, the ionic liquid [EMIM][BF4], although efficient as a masking agent, cannot be recommended as mobile phase additive to reproduce octanol–water partitioning. Copyright © 2010 John Wiley & Sons, Ltd.     

Some combinatorial principles for trees and applications to tree families in Banach spaces

Suppose that is a normalized family in a Banach space indexed by the dyadic tree S. Using Stern's combinatorial theorem we extend important results from sequences in Banach spaces to tree‐families. More precisely, assuming that for any infinite chain β of S the sequence is weakly null, we prove that there exists a subtree T of S such that for any infinite chain β of T the sequence is nearly (resp., convexly) unconditional. In the case where is a family of continuous functions, under some additional assumptions, we prove the existence of a subtree T of S such that for any infinite chain β of T, the sequence is unconditional. Finally, in the more general setting where for any chain β, is a Schauder basic sequence, we obtain a dichotomy result concerning the semi‐boundedly completeness of the sequences .     

Nucleophilic aryl fluorination and aryl halide exchange mediated by a Cu(I)/Cu(III) catalytic cycle

Copper-catalyzed halide exchange reactions under very mild reaction conditions are described for the first time using a family of model aryl halide substrates. All combinations of halide exchange (I, Br, Cl, F) are observed using catalytic amounts of Cu(I). Strikingly, quantitative fluorination of aryl-X substrates is also achieved catalytically at room temperature, using common F(-) sources, via the intermediacy of aryl-Cu(III)-X species. Experimental and computational data support a redox Cu(I)/Cu(III) catalytic cycle involving aryl-X oxidative addition at the Cu(I) center, followed by halide exchange and reductive elimination steps. Additionally, defluorination of the aryl-F model system can be also achieved with Cu(I) at room temperature operating under a Cu(I)/Cu(III) redox pair.     

Oligo(ethylene imine)-grafted glycidyl methacrylate linear and star homopolymers: Odd–even correlated transfection efficiency

The present study aims to investigate an odd–even effect of the number of ethylene imine units in the side-groups of totally abiotic synthetic polymers on their efficiency in DNA transfection. A library of fifteen polymers was fabricated. Two star homopolymers and one linear homopolymer based on glycidyl methacrylate were synthesized and used as precursors to which five linear oligo(ethylene imine)s (OEI) were grafted. The number of ethylene imine groups of the OEIs was varied. Specifically, ethylene diamine, diethylene triamine, triethylene tetramine, tetraethylene pentamine, and pentaethylene hexamine were used. Each of these fifteen OEI-grafted polymers was evaluated in terms of their efficiency to transfer plasmid DNA encoding firefly luciferase in C2C12 mouse myoblast cells. The transfection efficiency displayed an odd-even pattern, with all OEI-grafted polymers with an odd number of ethylene imine repeating units exhibiting higher transfection efficiency compared with those possessing an even number of ethylene imine repeating units. The odd–even effect was more pronounced for the star polymers with longer arms (degree of polymerization, DP = 100), while in case of the linear polymers, the odd–even effect was only observed for the lowest polymer loading. The cytotoxicity of the OEI-grafted polymers also followed an odd–even pattern, with the OEI-grafted star polymers with an arm DP of 100 and the linear polymers clearly presenting an odd-even effect, while the cytotoxicity of the OEI-grafted star polymers with an arm DP of 20 slightly increased with the number of ethylene imine repeating units.     

Synthesis and complete assignment of the 1H and 13C NMR spectra of 6-substituted and 2,6-disubstituted pyridazin-3(2H)-ones

Several pyridazin-3(2H)-one derivatives were synthesized starting from alkyl furans using oxidation with singlet oxygen to give 4-methoxy or 4-hydroxybutenolides, key intermediates of the synthetic strategy followed. For all pyridazinones reported, a complete assignment of the (1)H and (13)C NMR spectra using one- and two-dimensional NMR spectroscopic methods, which included NOE, DEPT, COSY, HSQC and HMBC experiments, was accomplished. Correlations between the chemical shifts of the heterocyclic ring atoms and substituents at N-2 and C-6 were analyzed.     

Selective Ortho‐Hydroxylation–Defluorination of 2‐Fluorophenolates with a Bis(μ‐oxo)dicopper(III) Species

The bis(μ‐oxo)dicopper(III) species [Cu^III₂(μ‐O)₂(m‐XYL^MeAN)]²⁺ ( 1 ) promotes the electrophilic ortho‐hydroxylation–defluorination of 2‐fluorophenolates to give the corresponding catechols, a reaction that is not accomplishable with a (η²:η²‐O₂)dicopper(II) complex. Isotopic labeling studies show that the incoming oxygen atom originates from the bis(μ‐oxo) unit. Ortho‐hydroxylation–defluorination occurs selectively in intramolecular competition with other ortho‐substituents such as chlorine or bromine.     

Readily Accessible Bulky Iron Catalysts exhibiting Site Selectivity in the Oxidation of Steroidal Substrates

Bulky iron complexes are described that catalyze the site‐selective oxidation of alkyl C?H bonds with hydrogen peroxide under mild conditions. Steric bulk at the iron center is introduced by appending trialkylsilyl groups at the meta‐position of the pyridines in tetradentate aminopyridine ligands, and this effect translates into high product yields, an enhanced preferential oxidation of secondary over tertiary C?H bonds, and the ability to perform site‐selective oxidation of methylenic sites in terpenoid and steroidal substrates. Unprecedented site selective oxidation at C6 and C12 methylenic sites in steroidal substrates is shown to be governed by the chirality of the catalysts.