Design and Synthesis of De Novo Peptide for Manganese Binding

The de novo peptide with 63-residues (MHB) has been synthesized biochemically and used for the binding of manganese (II) ions. In designed peptide, the leucine of the peptide dA1 (prototype) was replaced by His27 and Asp41 for binding the manganese (II) ions. The different chromatography studies and mass determination showed that new peptide folds into a monomeric, highly helical with a active site structure similar to the native Mn–SOD in an aqueous solution. Electron paramagnetic resonance (EPR) study suggested that the peptide binds single manganese (II) ion per molecule loosely with K _D value of about 36 μM. The circular dichroism (CD) studies demonstrated that the helical contents of the peptide did not change significantly even after binding the metal ions. The SOD activity study of the Mn–peptide complex showed that the IC₅₀ values is 8.08 μM.     

Evaluation of Chemical Derivatisation Methods for Protein Identification using MALDI MS/MS

In proteomic studies, assigning protein identity from organisms whose genomes are yet to be completely sequenced remains a challenging task. For these organisms, protein identification is typically based on cross species matching of amino acid sequence obtained from collision induced dissociation (CID) of peptides using mass spectrometry. The most direct approach of de novo sequencing is slow and often difficult, due to the complexity of the resultant CID spectra. For MALDI-MS, this problem has been addressed by using chemical derivatisation to direct peptide fragmentation, thereby simplifying CID spectra and facilitating de novo interpretation. In this study, milk whey proteins from the tammar wallaby (Macropus eugenii) were used to evaluate three chemical derivatisation methods compatible with MALDI MS/MS. These methods included (i) guanidination and sulfonation using chemically-assisted fragmentation (CAF), (ii) guanidination and sulfonation using 4-sulfophenyl isothiocyanate (SPITC) and (iii) derivatising the epsilon-amino group of lysine residues with Lys Tag 4H. Derivatisation with CAF and SPITC resulted in more protein identification than Lys Tag 4H. Sulfonation using SPITC was the preferred method due to the low cost per experiment, the reactivity with both lysine and arginine terminated peptides and the resultant simplified MS/MS spectra.*Australian Peptide Conference Issue.**This project was funded by an ARC Linkage grant to Deane supported by TGR Biosciences and facilitated by access to the Australian Proteome Analysis Facility established under the Australian Government’s Major National Research Facilities program.     

New proposals for naming lower-ranked taxa within the frame of the International Code of Zoological Nomenclature

The recent multiplication of cladistic hypotheses for many zoological groups poses a challenge to zoological nomenclature following the International Code of Zoological Nomenclature: in order to account for these hypotheses, we will need many more ranks than currently allowed in this system, especially in lower taxonomy (around the ranks genus and species). The current Code allows the use of as many ranks as necessary in the family-series of nomina (except above superfamily), but forbids the use of more than a few ranks in the genus and species-series. It is here argued that this limitation has no theoretical background, does not respect the freedom of taxonomic thoughts or actions, and is harmful to zoological taxonomy in two respects at least: (1) it does not allow to express in detail hypothesized cladistic relationships among taxa at lower taxonomic levels (genus and species); (2) it does not allow to point taxonomically to low-level differentiation between populations of the same species, although this would be useful in some cases for conservation biology purposes. It is here proposed to modify the rules of the Code in order to allow use by taxonomists of an indeterminate number of ranks in all nominal-series. Such an 'expanded nomenclatural system' would be highly flexible and likely to be easily adapted to any new finding or hypothesis regarding cladistic relationships between taxa, at genus and species level and below. This system could be useful for phylogeographic analysis and in conservation biology. In zoological nomenclature, whereas robustness of nomina is necessary, the same does not hold for nomenclatural ranks, as the latter are arbitrary and carry no special biological, evolutionary or other information, except concerning the mutual relationships between taxa in the taxonomic hierarchy. Compared to the Phylocode project, the new system is equally unambiguous within the frame of a given taxonomic frame, but it provides more explicit and informative nomina for non-specialist users, and is more economic in terms of number of nomina needed to account for a given hierarchy. These ideas are exemplified by a comparative study of three possible nomenclatures for the taxonomy recently proposed by Hillis and Wilcox (2005) for American frogs traditionally referred to the genus Rana.     

A hierarchical matrix model to assess the impact of habitat fragmentation on population dynamics: an elasticity analysis

To better understand the role of habitat quality and boundaries on population dynamics at the landscape scale, we develop a model combining a spatially implicit approach, a spatial population Leslie-type model and an implicit model of habitat fragmentation. An original approach of elasticity permits to identify which types of element and boundary influence the most population viability according to the wood fragmentation degree. The studied species is a corridor forest insect sensitive to fragmentation (Abax parallelepipedus, Coleoptera, Carabidae). We show that a single large patch of wood is better than several small patches for the population viability.     

Who was the first? An experimental application of carnivore and hominid overlapping marks at the Pleistocene archaeological sites

There are many types of evidence that provide information about methods for obtaining animal nutrients. Several researchers suggest that the main element to be considered is the skeletal representation of the different species identified in the faunal assemblage. This element must be associated to the animals’ age at death and the localisation of processing marks of the carcasses (both those of anthropic origin and those produced by carnivores). Occasionally, these marks coincide on the same point of the bone, giving cause for overlapping marks. These marks can be considered an aid more to identify the anthropic manner for obtaining animal recourses. However, these cases are very unusual at archaeological sites, and it is not always easy to identify which of the two predators has obtained the prey first. Through the experimental process presented in this article, we have observed diagnostic elements on overlapping marks that show the action sequence of the predators (hominids and carnivores) on carcasses. These experimental criteria were applied to different archaeological sites of the Lower and Middle Pleistocene in the Iberian Peninsula: Bolomor Cave (Valencia, Spain) and level TD10-1 and TD6-2 of Gran Dolina (Atapuerca, Burgos). In these assemblages, we were able to distinguish hunting and scavenging events through overlapping marks, providing a new element to the general interpretation of these sites.     

Brefeldin A inhibits expression of DNA packaging proteins and nucleocapsid formation of human cytomegalovirus

In this study we used the fungal antibiotic brefeldin A (BFA) to analyze its effect on viral replication. Analysis by electron microscopy demonstrated that no viral particles were observed in cells treated before the onset of viral replication. In the presence of BFA expression of IE2, MCP, pUL104, pUL56 and pUL89 were reduced, while no or slight effect was observed on expression of pp65, pUL44 and pUL57. Strikingly, real time PCR revealed that de novo viral DNA synthesis is reduced but not completely abolished in the presence of BFA. These results indicated that BFA represents a multi-functional compound leading to inhibition of several steps of viral maturation such as expression of viral DNA packaging proteins and capsid formation.     

Reduced insulin-mediated inhibition of VLDL secretion upon pharmacological activation of the liver X receptor in mice

The nuclear liver X receptor (LXR) regulates multiple aspects of cholesterol, triacylglycerol (TG), and carbohydrate metabolism. Activation of LXR induces the expression of genes encoding enzymes involved in de novo lipogenesis (DNL) resulting in hepatic steatosis in mice. Pharmacological LXR activation has also been reported to improve insulin sensitivity and glucose homeostasis in diabetic rodents. The effects of pharmacological LXR ligands on insulin''s action on hepatic lipid metabolism are not known. We evaluated secretion of VLDL during a hyperinsulinemic euglycemic clamp in mice treated with the LXR-ligand T0901317. In untreated mice, hyperinsulinemia reduced the availability of plasma NEFA for VLDL-TG synthesis, increased the contribution of DNL to VLDL-TG, reduced VLDL particle size, and suppressed overall VLDL-TG production rate by approximately 50%. Upon T0901317 treatment, hyperinsulinemia failed to reduce VLDL particle size or suppress VLDL-TG production rate, but the contribution of DNL to VLDL-TG was increased. In conclusion, the effects of LXR activation by T0901317 on lipid metabolism can override the normal control of insulin to suppress VLDL particle secretion.     

Pollen analysis from two littoral marshes (Bourdim and Garaat El-Ouez) in the El-Kala wet complex (North-East Algeria). Lateglacial and Holocene history of Algerian vegetation

The study of two pollen sequences from El-Kala marshes allowed the reconstruction of the regional vegetation history supported by eight radiocarbon dates. Pollen assemblages from Bourdim site were dominated by local input of Alnus and Salix, while regional vegetation was characterized by scattered Quercus suber forests with a well-developed Erica arborea matorral. While the vegetation dynamics recorded at Bourdim is recent (Late Holocene), the majority of the pollen diagram from Garaat El-Ouez is contemporaneous to the Late Pleniglacial and is characterized by open woodlands with Pinus, Poaceae and several heliophilous herbs. The significant values of Cedrus pollen identified in this period indicate that the region of El-Kala most probably played the role of a refugium for this tree.     

Structural refinement of the hERG1 pore and voltage‐sensing domains with ROSETTA‐membrane and molecular dynamics simulations

The hERG1 gene (Kv11.1) encodes a voltage‐gated potassium channel. Mutations in this gene lead to one form of the Long QT Syndrome (LQTS) in humans. Promiscuous binding of drugs to hERG1 is known to alter the structure/function of the channel leading to an acquired form of the LQTS. Expectably, creation and validation of reliable 3D model of the channel have been a key target in molecular cardiology and pharmacology for the last decade. Although many models were built, they all were limited to pore domain. In this work, a full model of the hERG1 channel is developed which includes all transmembrane segments. We tested a template‐driven de‐novo design with ROSETTA‐membrane modeling using side‐chain placements optimized by subsequent molecular dynamics (MD) simulations. Although backbone templates for the homology modeled parts of the pore and voltage sensors were based on the available structures of KvAP, Kv1.2 and Kv1.2‐Kv2.1 chimera channels, the missing parts are modeled de‐novo. The impact of several alignments on the structure of the S4 helix in the voltage‐sensing domain was also tested. Herein, final models are evaluated for consistency to the reported structural elements discovered mainly on the basis of mutagenesis and electrophysiology. These structural elements include salt bridges and close contacts in the voltage‐sensor domain; and the topology of the extracellular S5‐pore linker compared with that established by toxin foot‐printing and nuclear magnetic resonance studies. Implications of the refined hERG1 model to binding of blockers and channels activators (potent new ligands for channel activations) are discussed. Proteins 2010. © 2010 Wiley‐Liss, Inc.