Modeling spatial patterns in Dictyostelium

The life cycle of Dictyostelium discoideum provides a striking example of the transition from single cell behavior to multicellular cooperativity. In this paper the status of the attempts at making semiquantitative models of the aggregation phase of this cycle is reviewed. Specifically, it is discussed how the propagation of cAMP waves is a typical example of excitable signaling, which is then rendered unstable by coupling to cell chemotaxis. To investigate the streaming pattern that emerges from this clumping instability, we next turn to a new simulation strategy, which couples dynamical cell-like entities ("bions") to continuum chemical concentration fields. Finally, we discuss two directions for further research: One is the study of the robustness with respect to the variation of system parameters (such as the cell density) exhibited by the biological system, but not by any simple model. The other concerns going beyond the aggregation phase to tackle the three-dimensional problem of slug formation and motion.     

Toward understanding the ionization of biomarkers from micrometer particles by bio-aerosol mass spectrometry

The appearance of informative signals in the mass spectra of laser-ablated bio-aerosol particles depends on the effective ionization probabilities (EIP) of individual components during the laser ionization process. This study investigates how bio-aerosol chemical composition governs the EIP values of specific components and the overall features of the spectra from the bio-aerosol mass spectrometry (BAMS). EIP values were determined for a series of amino acid, dipicolinic acid, and peptide aerosol particles to determine what chemical features aid in ionization. The spectra of individual amino acids and dipicolinic acid, as well as mixtures, were examined for extent of fragmentation and the presence of molecular ion dimers, which are indicative of ionization conditions. Standard mixtures yielded information with respect to the significance of secondary ion plume reactions on observed spectra. A greater understanding of how these parameters affect EIP and spectra characteristics of bio-aerosols will aid in the intelligent selection of viable future biomarkers for the identification of bio-terrorism agents.     

Synthesis of homoallylic chiral tertiary alcohols via chelation-controlled diastereoselective nucleophilic addition on alpha-alkoxyketones: application for the synthesis of the C(1)-C(11) subunit of 8-epi-fostriecin

[reaction: see text] Chiral beta-syn-alkoxyhomoallylic alcohols derived from alkoxyallylboration of aldehydes upon oxidation provided the corresponding chiral ketones. Chelation-controlled nucleophilic addition to these ketones occurred in a highly stereoselective manner to afford anti-homoallylic tertiary alcohols. This methodology has been applied for the synthesis of the C(1)-C(11) subunit of C(8)-epi-fostriecin.     

Organoboranes—34 : General synthesis of chiral boronic and borinic esters via asymmetric hydroboration-displacement. carbenoidation of chiral borinic esters to acyclic ketones of high enantiomeric purities

Asymmetric hydroboration of appropriate alkenes with diisopinocampheylborane (Ipc₂BH) or monoisopinocampheylborane (IpcBH₂) produces intermediates that readily eliminate α-pinene on treat- ment with acetaldehyde, providing a direct, convenient route to chiral boronic esters of high enantiomeric purities. Mixed chiral trialkylboranes, readily prepared by stepwise hydroboration of appropriate alkenes with IpcBH₂, eliminate α-pinene on treatment with acetaldehyde under very mild conditions. The procedure makes readily available chiral borinic esters of high enantiomeric purities. The synthetic utility of chiral borinic esters is demonstrated by converting them into acyclic ketones including an alarm pheromone of the ant Monica mutica.     

Effects of thioamide substitutions on the conformation and stability of alpha- and 3(10)-helices

Thiopeptides, formed by replacing the amide oxygen atom with a sp(2) sulfur atom, are useful in protein engineering and drug design because they confer resistance to enzymatic degradation and are predicted to be more rigid. This report describes our free molecular dynamics simulations with explicit water and free energy calculations on the effects of thio substitutions on the conformation of alpha-helices, 3(10)-helices, and their relative stability. The most prominent structural effect of thio substitution is the increase in the hydrogen bond distance from 2.1 A for normal peptides to 2.7 A for thiopeptides. To accommodate for the longer C[double bond]S...H-N hydrogen bond, the (phi, psi) dihedral angles of the alpha-helix changed from (-66 degrees, -42 degrees) to (-68 degrees, -38 degrees), and the rise per turn increased from 5.5 to 6.3 A. For 3(10)-helices, the (phi, psi) dihedral angles (-60 degrees, -20 degrees) and rise per turn (6.0 A) changed to (-66 degrees, -12 degrees) and 6.8 A, respectively. In terms of relative stability, the most prominent change upon thio substitution is the decrease in the free energy difference, Delta A(alpha --> 3(10)), from 14 to 3.5 kcal/mol. Therefore, normal peptides are less likely to form 3(10)-helix than are thiopeptides. Component analysis of the Delta A(alpha --> 3(10)) reviews that the entropy advantage of the 3(10)-helix for both Ac-Ala(10)-NHMe and Act-Alat(10)-NHMe is attributed to the 3(10)-helix being more flexible than the alpha-helix. Interestingly, upon thio substitution, this differential flexibility is even more apparent because the alpha-helix conformation of Act-Alat(10)-NHMe becomes more rigid due to the bulkier sulfur atom.     

Isolierung und Struktur von Pteridinen (Lumazinen) aus Russula sp. (Täublinge; Basidiomycetes)

Isolation and Structure Elucidation of Pteridines (Lumazines) from Russula sp. (Basidiomycetes) Extensive chromatogaphic separations and spectroscopic investigations have led to the isolation and identification of several water-soluble pteridines from Russula sp., the so-called russupteridines, namely: 1-(5-amino-2-6-dioxo-1,2,3,6-tetrahydeopyrimidin-4-yl)amino-1-deoxy-D -ribitol ( 1 ; a pro-lumazine; first identification in a basidiomycete(; l-deoxy-l-(6-methyl-2-4,7-trioxo-1,2,3,4,7,8-hexahydro-pteridin-8-yl)-D -ribitol ( 3 ) and l-deoxy-1-(2,4,7-trioxo-1,2,3,4,7,8-hexahydeopteridin-8-yl)-D -ribitol ( 4 ); both compounds found for the first time in higher fungi; they belong to the components with the strongest violet-blue fluorescence in Russula sp.; riboflavine ( 6 ; now recognized as an important yellow colorant in a great many of Russula sp.); russupteridine-yellow I (= l-(6-amino-7-(N-fromylimino)-2,4-dioxo-1,2,3,4,7,8-hexahydropteridin-8-yl)-1-deoxy-D -ribitol; 5 ; a component with very strong fluorescence; the first derivative of the novel 6,7-diamino-lamazine); russupteridine-yellow IV (= l-deoxy-1-)(2,6,8-trioxo-2,4,5,6,7,8-hexahydro-1H-imidazolo[4,5-g]pteridin-4-yl)-D -ribitol (7)). Two further yellow russupteridines (yellow II and Yellow V) with very strong fluorescence have been isolated and characterized.