Determination of absolute ion yields from a MALDI source through calibration of an image-charge detector

MALDI (matrix-assisted laser desorption/ionization) is one of the most important techniques used to produce large biomolecular ions in the gas phase. Surprisingly, the exact ionization mechanism is still not well understood and absolute values for the ion yields are scarce. This is in part due to the unknown efficiencies of typical detectors, especially for heavy biomolecular ions. As an alternative, charged particles can be non-destructively detected using an image-charge detector where the output voltage signal is proportional to the total charge within the device. In this paper, we report an absolute calibration which provides the voltage output per detected electronic charge in our experimental arrangement. A minimum of 3 x 10(3) ions were required to distinguish the signal above background noise in a single pass through the device, which could be further reduced using filtering techniques. The calibration results have been applied to raw MALDI spectra to measure absolute ion yields of both matrix and analyte ions.

Gross anatomy and positional homology of gills, gonopores, and nephridiopores in “basal” living chitons (Polyplacophora: Lepidopleurina)

Traditional shell characters are insufficient to differentiate taxa within the polyplacophoran order Lepidopleurida. Additional morphological character sets from soft anatomy (e.g., gamete morphology, gill arrangement, and locations of gonopores and nephidiopores) have previously been described from only a small number of taxa. This study reports for the first time, positions of the gonopores and nephridiopores for 17 species in the Lepidopleurina. The position of both types of pores on the longitudinal body axis varies within a generalized range of the posterior third of the body; however, the separation between the pores as a proportion of the specimen’s foot length varies from 3.7% to 17% in different species. Positions of pores relative to the serial gills are also variable within species, and future studies may require a new descriptive basis in order to resolve positional homology. The order Lepidopleurida occupies a critical position with respect to understanding larger-scale patterns in polyplacophoran (and molluscan) evolution.

Mesophases in Nearly 2D Room-Temperature Ionic Liquids

Computer simulations of (i) a [C(12)mim][Tf2N] film of nanometric thickness squeezed at kbar pressure by a piecewise parabolic confining potential reveal a mesoscopic in-plane density and composition modulation reminiscent of mesophases seen in 3D samples of the same room-temperature ionic liquid (RTIL). Near 2D confinement, enforced by a high normal load, as well as relatively long aliphatic chains are strictly required for the mesophase formation, as confirmed by computations for two related systems made of (ii) the same [C(12)mim][Tf2N] adsorbed at a neutral solid surface and (iii) a shorter-chain RTIL ([C(4)mim][Tf2N]) trapped in the potential well of part i. No in-plane modulation is seen for ii and iii. In case ii, the optimal arrangement of charge and neutral tails is achieved by layering parallel to the surface, while, in case iii, weaker dispersion and packing interactions are unable to bring aliphatic tails together into mesoscopic islands, against overwhelming entropy and Coulomb forces. The onset of in-plane mesophases could greatly affect the properties of long-chain RTILs used as lubricants.

Study of the intergrain interaction potential and associated instability of dust-lattice plasma oscillations in the presence of ion flow

A comprehensive study of the Debye-Huckel repulsive and ion wakefield induced attractive potentials around a dust grain is presented, including ion flow. It is found that the modified interaction potential (especially the attractive wakefield force) can cause instability of linear dust oscillations propagating in a dusty plasma crystal composed of dust grains in a horizontal arrangement suspended in the sheath region near a conducting wall (electrode). The dependence of dust lattice modes on the ion flow is studied, revealing instability of dust lattice modes for certain values of the ion flow speed. (C) 2003 Elsevier B.V. All rights reserved.

A molecular model for drug binding to tandem repeats of telomeric G-quadruplexes.

The extreme 3'-ends of human telomeres consist of 150–250 nucleotides of single-stranded DNA sequence together with associated proteins. Small-molecule ligands can compete with these proteins and induce a conformational change in the DNA to a four-stranded quadruplex arrangement, which is also no longer a substrate for the telomerase enzyme. The modified telomere ends provide signals to the DNA-damage-response system and trigger senescence and apoptosis. Experimental structural data are available on such quadruplex complexes comprising up to four telomeric DNA repeats, but not on longer systems that are more directly relevant to the single-stranded overhang in human cells. The present paper reports on a molecular modelling study that uses Molecular Dynamics simulation methods to build dimer and tetramer quadruplex repeats. These incorporate ligand-binding sites and are models for overhang–ligand complexes.

Far field subwavelength source resolution using Phase Conjugating Lens Assisted With Evanescent-to-Propagating Spectrum Conversion

The imaging properties of a phase conjugating lens operating in the far field zone of the imaged source and augmented with scatterers positioned in the source near field region are theoretically studied in this paper. The phase conjugating lens consists of a double sided 2D assembly of straight wire elements, individually interconnected through phase conjugation operators. The scattering elements are straight wire segments which are loaded with lumped impedance loads at their centers. We analytically and numerically analyze all stages of the imaging process; i) evanescent-to-propagating spectrum conversion; ii) focusing properties of infinite or finite sized phase conjugating lens; iii) source reconstruction upon propagating-to-evanescent spectrum conversion. We show that the resolution that can be achieved depends critically on the separation distance between the imaged source and scattering arrangement, as well as on the topology of the scatterers used. Imaged focal widths of up to one-seventh wavelength are demonstrated. The results obtained indicate the possibility of such an arrangement as a potential practical means for realising using conventional materials devices for fine feature extraction by electromagnetic lensing at distances remotely located from the source objects under investigation

Identification of a major GpVI-binding locus in human type III collagen

We have analyzed the adhesion of human and murine platelets, and of recombinant human and murine GpVI ectodomains, to synthetic triple-helical collagen-like peptides. These included 57 peptides derived from the sequence of human type III collagen and 9 peptides derived from the cyanogen bromide fragment of bovine type III collagen, alpha 1(III)CB4. We have identified several peptides that interact with GpVI, in particular a peptide designated III-30 with the sequence GAOGLRGGAGPOG-PEGGKGAAGPOGPO. Both human and murine platelets bound to peptide III-30 in a GpVI-dependent manner. III-30 also supported binding of recombinant GpVI ectodomains. Cross-linked III-30 induced aggregation of human and murine platelets, although with a lower potency than collagen-related peptide. Modifications of the peptide sequence indicated that the hydroxyproline residues play a significant role in supporting its GpVI reactivity. However, many peptides containing OGP/ GPO motifs did not support adhesion to GpVI. These data indicate that the ability of a triple-helical peptide to bind GpVI is not solely determined by the presence or spatial arrangement of these OGP/GPO motifs within the peptides.

Structural basis for the platelet-collagen interaction - The smallest motif within collagen that recognizes and activates platelet glycoprotein VI contains two glycine-proline-hydroxyproline triplets

Collagen-related peptide is a selective agonist for the platelet collagen receptor Glycoprotein VI. The triple helical peptide contains ten GPO triplets/strand (single letter amino acid nomenclature, where O is hydroxyproline) and so over-represents GPO compared with native collagen sequence. To investigate the ability of Glycoprotein VI to recognize GPO triplets in a setting more representative of the collagens, we synthesized a set of triple helical peptides containing fewer GPO triplets, varying their number and spacing within an inert (GPP)(n) backbone. The adhesion of recombinant human Glycoprotein VI ectodomain, like that of human platelets, to these peptides increased with their GPO content, and platelet adhesion was abolished by the specific anti-Glycoprotein VI-blocking antibody, 10B12. Platelet aggregation and protein tyrosine phosphorylation were induced only by cross-linked peptides and only those that contained two or more GPO triplets. Such peptides were less potent than cross-linked collagen-related peptide. Our data suggest that both the sequences GPOGPO and GPO center dot center dot center dot center dot center dot center dot center dot center dot center dot GPO represent functional Glycoprotein VI recognition motifs within collagen. Furthermore, we propose that the (GPO)(4) motif can support simultaneous binding of two glycoprotein VI molecules, in either a parallel or anti-parallel stacking arrangement, which could play an important role in activation of signaling.

A comparison of nonstaggered compact FDTD schemes for the 3D wave equation

This paper aims at providing a better insight into the 3D approximations of the wave equation using compact finite-difference time-domain (FDTD) schemes in the context of room acoustic simulations. A general family of 3D compact explicit and implicit schemes based on a nonstaggered rectilinear grid is analyzed in terms of stability, numerical error, and accuracy. Various special cases are compared and the most accurate explicit and implicit schemes are identified. Further considerations presented in the paper include the direct relationship with other numerical approaches found in the literature on room acoustic modeling such as the 3D digital waveguide mesh and Yee's staggered grid technique.

Protein surface recognition using geometrically pure Ru(II) tris(bipyridine) derivatives

This manuscript illustrates that the geometric arrangement of protein-binding groups around a ruthenium(II) core leads to dramatic differences in cytochrome c (cyt c) binding highlighting that it is possible to define synthetic receptors with shape complementarity to protein surfaces.

Mesoscale flux-closure domain formation in single-crystal BaTiO3

Over 60 years ago, Charles Kittel predicted that quadrant domains should spontaneously form in small ferromagnetic platelets. He expected that the direction of magnetization within each quadrant should lie parallel to the platelet surface, minimizing demagnetizing fields, and that magnetic moments should be configured into an overall closed loop, or flux-closure arrangement. Although now a ubiquitous observation in ferromagnets, obvious flux-closure patterns have been somewhat elusive in ferroelectric materials. This is despite the analogous behaviour between these two ferroic subgroups and the recent prediction of dipole closure states by atomistic simulations research. Here we show Piezoresponse Force Microscopy images of mesoscopic dipole closure patterns in free-standing, single-crystal lamellae of BaTiO3. Formation of these patterns is a dynamical process resulting from system relaxation after the BaTiO3 has been poled with a uniform electric field. The flux-closure states are composed of shape conserving 90° stripe domains which minimize disclination stresses.

Functional and Structural Diversification of the Anguimorpha Lizard Venom System

Venom has only been recently discovered to be a basal trait of the Anguimorpha lizards. Consequently, very little is known about the timings of toxin recruitment events, venom protein molecular evolution, or even the relative physical diversifications of the venom system itself. A multidisciplinary approach was used to examine the evolution across the full taxonomical range of this similar to 130 million-year-old clade. Analysis of cDNA libraries revealed complex venom transcriptomes. Most notably, three new cardioactive peptide toxin types were discovered (celestoxin, cholecystokinin, and YY peptides). The latter two represent additional examples of convergent use of genes in toxic arsenals, both having previously been documented as components of frog skin defensive chemical secretions. Two other novel venom gland-overexpressed modified versions of other protein frameworks were also recovered from the libraries (epididymal secretory protein and ribonuclease). Lectin, hyaluronidase, and veficolin toxin types were sequenced for the first time from lizard venoms and shown to be homologous to the snake venom forms. In contrast, phylogenetic analyses demonstrated that the lizard natriuretic peptide toxins were recruited independently of the form in snake venoms. The de novo evolution of helokinestatin peptide toxin encoding do-mains within the lizard venom natriuretic gene was revealed to be exclusive to the helodermatid/anguid subclade. New isoforms were sequenced for cysteine-rich secretory protein, kallikrein, and phospholipase A 2 toxins. Venom gland morphological analysis revealed extensive evolutionary tinkering. Anguid glands are characterized by thin capsules and mixed glands, serous at the bottom of the lobule and mucous toward the apex. Twice, independently this arrangement was segregated into specialized serous protein-secreting glands with thick capsules with the mucous lobules now distinct (Heloderma and the Lanthanotus/Varanus clade). The results obtained highlight the importance of utilizing evolution-based search strategies for biodiscovery and emphasize the largely untapped drug design and development potential of lizard venoms. Molecular & Cellular Proteomics 9:2369-2390, 2010.

Assembly of a coordination cage with four aromatic channel receptors on the outside

Silver salts and triphosphine ligands with biphenyl substituents assemble to give coordination cages with four external aromatic channel receptors in a pseudo-tetrahedral arrangement.

Novel pyridyl-stabilised rigid-rod organometallic polymers and their monomeric precursors

Reaction of trans-[Pt(NC5H4CHBu2n)(2)Cl-2] 1 with an excess of HC=CR (R = Ph, C6H4Me, C6H4NO2) affords the monomeric complex trans-[Pt(NC5H4CHBu2n)(2)(C=CR)(2)] (R = Ph 2a, C6H4Me 2b, C6H4NO2 2c), the trans arrangement of the alkynyl ligands being confirmed from spectroscopic data and by an X-ray analysis of 2c;when 1 is treated with 1 equiv, of HC=CC6H2(Me)(2)C=CH the polymer [Pt(NC5H4CHBu2n)(2)C=CC6H2Me2C=C](n) is formed, which is soluble in a range of organic solvents.

Lateralization of lateral displays in convict cichlids

We examine lateralization of lateral displays in convict cichlids, Amatitlania nigrofasciata, and show a population level preference for showing the right side. This enables contesting pairs of fish to align in a head-to-tail posture, facilitating other activities. We found individuals spent a shorter mean time in each left compared with each right lateral display. This lateralization could lead to contesting pairs using a convention to align in a predictable head-to-tail arrangement to facilitate the assessment of fighting ability. It has major implications for the common use of mirror images to study fish aggression, because the 'opponent' would never cooperate and would consistently show the incorrect side when the real fish shows the correct side. With the mirror, the 'normal' head-to-tail orientation cannot be achieved.