Mass spectrometric investigation of the DNA-binding properties of an anthracycline with two trisaccharide chains

Cosmomycin D (CosD) is an anthracycline that has two trisaccharide chains linked to its ring system. Gel electrophoresis showed that CosD formed stable complexes with plasmid DNA under conditions where daunorubicin (Dn) and doxorubicin (Dx) dissociated to some extent during the experiments. The footprint and stability of CosD complexed with 10- and 16 trier DNA was investigated using several applications of electrospray ionisation mass spectrometry (ESI-MS). ESI-MS binding profiles showed that fewer CosD molecules bound to the sequences than Dn or Dx. In agreement with this, ESI-MS analysis of nuclease digestion products of the complexes showed that CosD protected the DNA to a greater extent than Dn or Dx. In tandem MS experiments, all CosD-DNA complexes were more stable than Dn- and Dx-DNA complexes. These results Support that CosD binds more tightly to DNA and exerts a larger footprint than ESI-MS investigations of the binding properties of CosD Could be carried out rapidly and using only small amounts of sample. (C) 2008 Elsevier Inc. All rights reserved.

Recovery and upgrading bovine rumen protein by extrusion: Effect of lipid content on protein disulphide cross-linking, solubility and molecular weight

Bovine rumen protein with two levels of residual lipids (1.9% or 3.8%) was subjected to thermoplastic extrusion under different temperatures and moisture contents. Protein Solubility in different buffers, disulphide cross-linking and molecular weight distribution were determined on the extrudates. After extrusion, samples with 1.9% residual lipids content had a higher concentration of protein insoluble by undetermined forces, irrespective of feed moisture and processing temperature used. Lipid content of 3.8% in the feed material resulted in more protein participating in the extrudate network through non-covalent interactions (hydrophobic and electrostatic) and disulphide bonds. A small dependency of the extrusion process on moisture and temperature and a marked dependency on lipid content, especially phospholipid, was observed, Electrophoresis under non-reducing conditions showed that protein extrusion with low feed moisture promoted high molecular breakdown inside the barrel, probably due to intense shear force, and further protein aggregation at the die end. (C) 2009 Elsevier Ltd. All rights reserved.

A non-parametric vessel detection method for complex vascular structures

Modern medical imaging techniques enable the acquisition of in vivo high resolution images of the vascular system. Most common methods for the detection of vessels in these images, such as multiscale Hessian-based operators and matched filters, rely on the assumption that at each voxel there is a single cylinder. Such an assumption is clearly violated at the multitude of branching points that are easily observed in all, but the Most focused vascular image studies. In this paper, we propose a novel method for detecting vessels in medical images that relaxes this single cylinder assumption. We directly exploit local neighborhood intensities and extract characteristics of the local intensity profile (in a spherical polar coordinate system) which we term as the polar neighborhood intensity profile. We present a new method to capture the common properties shared by polar neighborhood intensity profiles for all the types of vascular points belonging to the vascular system. The new method enables us to detect vessels even near complex extreme points, including branching points. Our method demonstrates improved performance over standard methods on both 2D synthetic images and 3D animal and clinical vascular images, particularly close to vessel branching regions. (C) 2008 Elsevier B.V. All rights reserved.

Complex rearrangements in patients with duplications of MECP2 can occur by fork stalling and template switching

Duplication at the Xq28 band including the MECP2 gene is one of the most common genomic rearrangements identified in neurodevelopmentally delayed males. Such duplications are non-recurrent and can be generated by a non-homologous end joining (NHEJ) mechanism. We investigated the potential mechanisms for MECP2 duplication and examined whether genomic architectural features may play a role in their origin using a custom designed 4-Mb tiling-path oligonucleotide array CGH assay. Each of the 30 patients analyzed showed a unique duplication varying in size from similar to 250 kb to similar to 2.6 Mb. Interestingly, in 77% of these non-recurrent duplications, the distal breakpoints grouped within a 215 kb genomic interval, located 47 kb telomeric to the MECP2 gene. The genomic architecture of this region contains both direct and inverted low-copy repeat (LCR) sequences; this same region undergoes polymorphic structural variation in the general population. Array CGH revealed complex rearrangements in eight patients; in six patients the duplication contained an embedded triplicated segment, and in the other two, stretches of non-duplicated sequences occurred within the duplicated region. Breakpoint junction sequencing was achieved in four duplications and identified an inversion in one patient, demonstrating further complexity. We propose that the presence of LCRs in the vicinity of the MECP2 gene may generate an unstable DNA structure that can induce DNA strand lesions, such as a collapsed fork, and facilitate a Fork Stalling and Template Switching event producing the complex rearrangements involving MECP2.

The competing roles of extensional viscosity and normal stress differences in complex flows of elastic liquids

In various attempts to relate the behaviour of highly-elastic liquids in complex flows to their rheometrical behaviour, obvious candidates for study have been the variation of shear viscosity with shear rate, the two normal stress differences N(1) and N(2) especially N(1), and the extensional viscosity eta(E). In this paper, we shall be mainly interested in `constant-viscosity` Boger fluids, and, accordingly, we shall limit attention to N(1) and eta(E). We shall concentrate on two important flows - axisymmetric contraction flow and ""splashing"" (particularly that which arises when a liquid drop falls onto the free Surface of the same liquid). Modem numerical techniques are employed to provide the theoretical predictions. It is shown that the two obvious manifestations of viscoelastic rheometrical behaviour can sometimes be opposing influences in determining flow characteristics. Specifically, in an axisymmetric contraction flow, high eta(E) , can retard the flow, whereas high N(1) can have the opposite effect. In the splashing experiment, high eta(E) can certainly reduce the height of the so-called Worthington jet, thus confirming some early suggestions, but, again, other rheometrical influences can also have a role to play and the overall picture may not be as clear as it was once envisaged.

A Trotter-Kato product formula for a class of non-autonomous evolution equations

In this article dedicated to Professor V. Lakshmikantham on the occasion of the celebration of his 84th birthday, we announce new results concerning the existence and various properties of an evolution system UA+B(t, s)(0 <= s <= t <= T) generated by the sum -(A(t)+B(t)) of two linear, time-dependent and generally unbounded operators defined on time-dependent domains in a complex and separable Banach space B. In particular, writing G(B) for the algebra of all linear bounded operators on B, we can express UA+B(t, s)(0 <= s <= t <= T) as the strong limit in L(B) of a product of the holomorphic contraction semigroups generated by -A(t) and -B(t), thereby getting a product formula of the Trotter-Kato type under very general conditions which allow the domain D(A(t)+B(t)) to evolve with time provided there exists a fixed set D subset of boolean AND D-t epsilon[0,D-T](A(t)+B(t)) everywhere dense in B. We then mention several possible applications of our product formula to various classes of non-autonomous parabolic initial-boundary value problems, as well as to evolution problems of Schrodinger type related to the theory of time-dependent singular perturbations of self-adjoint operators in quantum mechanics. We defer all the proofs and all the details of the applications to a separate publication. (C) 2008 Elsevier Ltd. All rights reserved.

Accessibility in complex networks

This Letter describes a method for the quantification of the diversity of non-linear dynamics in complex networks as a consequence of self-avoiding random walks. The methodology is analyzed in the context of theoretical models and illustrated with respect to the characterization of the accessibility in urban streets. (C) 2008 Elsevier B.V. All rights reserved.

Concentric characterization and classification of complex network nodes: Application to an institutional collaboration network

Differently from theoretical scale-free networks, most real networks present multi-scale behavior, with nodes structured in different types of functional groups and communities. While the majority of approaches for classification of nodes in a complex network has relied on local measurements of the topology/connectivity around each node, valuable information about node functionality can be obtained by concentric (or hierarchical) measurements. This paper extends previous methodologies based on concentric measurements, by studying the possibility of using agglomerative clustering methods, in order to obtain a set of functional groups of nodes, considering particular institutional collaboration network nodes, including various known communities (departments of the University of Sao Paulo). Among the interesting obtained findings, we emphasize the scale-free nature of the network obtained, as well as identification of different patterns of authorship emerging from different areas (e.g. human and exact sciences). Another interesting result concerns the relatively uniform distribution of hubs along concentric levels, contrariwise to the non-uniform pattern found in theoretical scale-free networks such as the BA model. (C) 2008 Elsevier B.V. All rights reserved.

Estimating complex cortical networks via surface recordings-A critical note

We discuss potential caveats when estimating topologies of 3D brain networks from surface recordings. It is virtually impossible to record activity from all single neurons in the brain and one has to rely on techniques that measure average activity at sparsely located (non-invasive) recording sites Effects of this spatial sampling in relation to structural network measures like centrality and assortativity were analyzed using multivariate classifiers A simplified model of 3D brain connectivity incorporating both short- and long-range connections served for testing. To mimic M/EEG recordings we sampled this model via non-overlapping regions and weighted nodes and connections according to their proximity to the recording sites We used various complex network models for reference and tried to classify sampled versions of the ""brain-like"" network as one of these archetypes It was found that sampled networks may substantially deviate in topology from the respective original networks for small sample sizes For experimental studies this may imply that surface recordings can yield network structures that might not agree with its generating 3D network. (C) 2010 Elsevier Inc All rights reserved

Crystallographic Structure of Phosphofructokinase-2 from Escherichia coli in Complex with Two ATP Molecules. Implications for Substrate Inhibition

Phosphofructokinase-1 and -2 (Pfk-1 and Pfk-2, respectively) from Escherichia coli belong to different homologous superfamilies. However, in spite of the lack of a common ancestor, they share the ability to catalyze the same reaction and are inhibited by the substrate MgATP. Pfk-2, an ATP-dependent 6-phosphofructokinase member of the ribokinase-like superfamily, is a homodimer of 66 kDa subunits whose oligomerization state is necessary for catalysis and stability. The presence of MgATP favors the tetrameric form of the enzyme. In this work, we describe the structure of Pfk-2 in its inhibited tetrameric form, with each subunit bound to two ATP molecules and two Mg ions. The present structure indicates that substrate inhibition occurs due to the sequential binding of two MgATP molecules per subunit, the first at the usual site occupied by the nucleotide in homologous enzymes and the second at the allosteric site, making a number of direct and Mg-mediated interactions with the first. Two configurations are observed for the second MgATP, one of which involves interactions with Tyr23 from the adjacent subunit in the dimer and the other making an unusual non-Watson-Crick base pairing with the adenine in the substrate ATP. The oligomeric state observed in the crystal is tetrameric, and some of the structural elements involved in the binding of the Substrate and allosteric ATPs are also participating in the dimer-dimer interface. This structure also provides the grounds to compare analogous features of the nonhomologous phosphofructokinases from E. coli. (C) 2008 Elsevier Ltd. All rights reserved.

Alkaline magmatism in the Amambay area, NE Paraguay: The Cerro Sarambi complex

The Early Cretaceous alkaline magmatism in the northeastern region of Paraguay (Amambay Province) is represented by stocks, plugs, dikes, and dike swarms emplaced into Carboniferous to Triassic-Jurassic sediments and Precambrian rocks. This magmatism is tectonically related to the Ponta Pora Arch, a NE-trending structural feature, and has the Cerro Sarambi and Cerro Chiriguelo carbonatite complexes as its most significant expressions. Other alkaline occurrences found in the area are the Cerro Guazu and the small bodies of Cerro Apua, Arroyo Gasory, Cerro Jhu, Cerro Tayay, and Cerro Teyu. The alkaline rocks comprise ultramafic-mafic, syenitic, and carbonatitic petrographic associations in addition to lithologies of variable composition and texture occurring as dikes; fenites are described in both carbonatite complexes. Alkali feldspar and clinopyroxene, ranging from diopside to aegirine, are the most abundant minerals, with feldspathoids (nepheline, analcime), biotite, and subordinate Ti-rich garnet; minor constituents are Fe-Ti oxides and cancrinite as the main alteration product from nepheline. Chemically, the Amambay silicate rocks are potassic to highly potassic and have miaskitic affinity, with the non-cumulate intrusive types concentrated mainly in the saturated to undersaturated areas in silica syenitic fields. Fine-grained rocks are also of syenitic affiliation or represent more mafic varieties. The carbonatitic rocks consist dominantly of calciocarbonatites. Variation diagrams plotting major and trace elements vs. SiO(2) concentration for the Cerro Sarambi rocks show positive correlations for Al(2)O(3), K(2)O, and Rb, and negative ones for TiO(2), MgO, Fe(2)O(3), CaO, P(2)O(5), and Sr, indicating that fractional crystallization played an important role in the formation of the complex. Incompatible elements normalized to primitive mantle display positive spikes for Rb, La, Pb, Sr, and Sm, and negative for Nb-Ta, P, and Ti, as these negative anomalies are considerably more pronounced in the carbonatites. Chondrite-normalized REE patterns point to the high concentration of these elements and to the strong LRE/HRE fractionation. The Amambay rocks are highly enriched in radiogenic Sr and have T(DM) model ages that vary from 1.6 to 1.1 Ga. suggesting a mantle source enriched in incompatible elements by metasomatic events in Paleo-Mesoproterozoic times. Data are consistent with the derivation of the Cerro Sarambi rocks from a parental magma of lamprophyric (minette) composition and suggest an origin by liquid immiscibility processes for the carbonatites. (C) 2011 Elsevier Ltd. All rights reserved.

A ditryptophan cross-link is responsible for the covalent dimerization of human superoxide dismutase 1 during its bicarbonate-dependent peroxidase activity

Unlike intermolecular disulfide bonds, other protein cross-links arising from oxidative modifications cannot be reversed and are presumably more toxic to cells because they may accumulate and induce protein aggregation. However, most of these irreversible protein cross-links remain poorly characterized. For instance, the antioxidant enzyme human superoxide dismutase 1 (hSod1) has been reported to undergo non-disulfide covalent dimerization and further oligomerization during its bicarbonate-dependent peroxidase activity. The dimerization was shown to be dependent on the oxidation of the single, solvent-exposed TrP(32) residue of hSod1, but the covalent dimer was not isolated nor was its structure determined. In this work, the hSod1 covalent dimer was isolated, digested with trypsin in H(2)O and H(2)(18)O, and analyzed by UV-Vis spectroscopy and mass spectrometry (MS). The results demonstrate that the covalent dimer consists of two hSod1 subunits cross-linked by a ditryptophan, which contains a bond between C3 and N1 of the respective Trp(32) residues. We further demonstrate that the cross-link cleaves under usual MS/MS conditions leading to apparently unmodified Trp(32), partially hinders proteolysis, and provides a mechanism to explain the formation of hSod1 covalent trimers and tetramers. This characterization of the covalent hSod1 dimer identifies a novel oxidative modification of protein Trp residues and provides clues for studying its occurrence in vivo. (C) 2010 Elsevier Inc. All rights reserved.