New species of the genera Dryophthorus Germ. and Stenommatus Woll. (Coleoptera: Dryophthoridae) in Dominican amber

A new species of Dryophthorus and two new species of Stenommatus (Coleoptera: Dryophthoridae) are described from Dominican amber. Dryophthorus microtremus n. sp. is characterised by monochrome dorsal scales, nearly parallel sides of the pronotum, wide elytral intervals and the elytral apex only slightly narrowed. Stenommatus tanyrhinus n. sp. is characterised by an elongate rostrum 4.5 times as long as wide in the middle. S. leptorhinus is characterised by small body size, a thin rostrum 3.0 times as long as wide in the middle, wide striae and a narrow prosternal process. This brings the total number of species of Dryophthorini in Dominican amber to five, which is more than half the number of extant species.http://www.zoobank.org/urn:lsid:zoobank.org:pub:4329D0DA-57BD-4CEA-9464-ABD5D1577FC9     

Evaluating the stability of disulfide bridges in proteins: a torsional potential energy surface for diethyl disulfide

Disulfide bonds formed by the oxidation of cysteine residues in proteins are the major form of intra- and inter-molecular covalent linkages in the polypeptide chain. To better understand the conformational energetics of this linkage, we have used the MP2(full)/6-31G(d) method to generate a full potential energy surface (PES) for the torsion of the model compound diethyl disulfide (DEDS) around its three critical dihedral angles (χ₂, χ₃, χ₂′). The use of ten degree increments for each of the parameters resulted in a continuous, fine-grained surface. This allowed us to accurately predict the relative stabilities of disulfide bonds in high resolution structures from the Protein Data Bank. The MP2(full) surface showed significant qualitative differences from the PES calculated using the Amber force field. In particular, a different ordering was seen for the relative energies of the local minima. Thus, Amber energies are not reliable for comparison of the relative stabilities of disulfide bonds. Surprisingly, the surface did not show a minimum associated with χ₂～ ? 60°, χ₃～90, χ₂′～ ? 60°. This is due to steric interference between Hα atoms. Despite this, significant populations of disulfides were found to adopt this conformation. In most cases this conformation is associated with an unusual secondary structure motif, the cross-strand disulfide. The relative instability of cross-strand disulfides is of great interest, as they have the potential to act as functional switches in redox processes.     

The structure of N δ -( N ′-sulfodiaminophosphinyl)- l -ornithine and its binding to ornithine transcarbamoylase: A quantum chemical study

The structure of N i -( N '-Sulfodiaminophosphinyl)- l -ornithine (PSOrn) in complex with the enzyme ornithine transcarbamoylase (OTCase) was recently characterised by Langley et al. [D.B. Langley, M.D. Templeton, B.A. Fields, R.E. Mitchell and C.A. Collyer, J. Biol. Chem., 275 (2000) 20012] using X-ray diffraction techniques. In this work, the interaction of PSOrn with the arginine residues of OTCase is modelled using density functional theory, with an emphasis on characterising the mechanism of binding between PSOrn, an inhibitor, and the enzyme. For the purposes of this study, the interaction of PSO, an analogue of PSOrn (obtained by replacing a (CH 2 ) 3 CH( CO 2 m )( NH 3 + ) side chain by methyl) with one and two arginine (Arg) molecules are investigated. The PSO > (Arg) 2 trimer is found to be strongly bound, by ～171 kJ mol m 1 , due to the presence of four hydrogen bonds in addition to a large ionic interaction between a dinegative PSO 2 m and protonated arginines. The computed geometry is consistent with the X-ray structure and the large binding energy is consistent with the observation that PSOrn is a powerful inhibitor. Furthermore, in agreement with the proposals of Langley et al. , the most stable bound form of PSO is found to be an imino type tautomer. The population analyses that were carried out on PSO suggest that PN, PO, SN and SO bonds, as in a range of other systems, are generally either single or semipolar bonds.     

From “Haus Tambaran” to Church: Continuity and Change in Contemporary Papua New Guinean Architecture

ABSTRACT

This article examines contemporary Papua New Guinean architecture created in the oscillation between Melanesian culture and Western impact. Some of the country's indigenous buildings are truly remarkable, especially the prestigious structures known as “Haus Tambaran” in the Sepik River area which have lent inspiration to many outstanding samples of contemporary Papua New Guinean design. We have studied both the indigenous and contemporary architecture of the Sepik region in the field and in additional research in collaboration with the late Professor Wallace Ruff and are comparing and contrasting contemporary architectural design with indigenous buildings. Here, we focus on a church at Ambunti, East Sepik Province. There is no electricity available on the site to facilitate climate control. Moreover, this contemporary building serves Western political, social, religious and educational functions. At the same time, the church incorporates aspects of the country's architectural heritage, including aesthetics as well as site-design and design with climate. Our comparison contrasts the modern building's functions, aesthetics, and design solutions with the area's indigenous local equivalent, the Haus Tambaran, and reveals elements borrowed, left aside, or altered in the process of adaptation. Issues discussed here include historic precedent, aesthetics, ownership, gender, and other social issues, as well as design and construction. Formal aspects, their meanings and functions, as well as environmental considerations and design solutions are borrowed, translated, or transformed, recalling but also differing from “Green Architecture,” to serve contemporary Western needs.     

Biotechnological Production of Plant-Based Insecticides

ABSTRACT:?

The demand for natural and nonpersistent insecticides is increasing day by day. Plant cell cultures could be an alternative to conventional methods of production of insecticides from field-grown plants. In vitro cultured plant cells produce a wide array of insecticides as a part of their secondary metabolism. Their ability to synthesize key enzymes and the manipulation of these could lead to the enhanced production of many insecticides of industrial importance. The development of a high-yielding hairy root culture system for thiophenes, nicotine, and phytoecdysones is of considerable interest. In this article, the current literature on various factors that influence the growth, production, and secretion of six insecticidal compounds, namely, pyrethrins, azadirachtin, thiophenes, nicotine, rotenoids, and phytoecdysones which have been prospects for the scale-up of cell cultures, genetic engineering to obtain transgenic plants, and metabolically engineered plants for increased production of bio-molecules, has been discussed. Environmental safety clearance and the future prospects of application of bio-molecules for plant-derived insecticides are presented.     

3 Origins and evolution of the translation machinery

The protein synthesis machinery largely evolved prior to the last common ancestor and hence its study can provide insight to early events in the origin of life, including the transition from the hypothetical RNA world to living systems as we know them. By utilizing information from primary sequences, atomic resolution structures, and functional properties of the various components, it is possible to identify timing relationships (Hsiao et al., 2009; Fox, 2010). Taken together, these timing events are used to develop a preliminary time line for major evolutionary events leading to the modern protein synthesis machinery. It has been argued that a key initial event was the hybridization of two or more RNAs that created the peptidyl transferase center, (PTC), of the ribosome (Agmon et al. 2005). The PTC, left side of figure, contains a characteristic cavity/pore that serves as the entrance to the exit tunnel and is thought to be essential to the catalysis (Fox et al., 2012). This cavity is distinct from typical RNA pores (right side of figure) in that the nitrogenous bases face towards the lumen of the pore and thus are available for hydrogen bonding interactions. In typical RNA pores, the bases carefully avoid the lumen region. In support of Agmon et al. 2005), it is argued that this key difference reflects the fact the pore was created by an early hybridization event rather than normal RNA folding.     

The Conformational Analysis of Substance P Analogs Using High-Field NMR Techniques

Abstract

High-field nuclear magnetic resonance measurements were carried out on substance P fragments SP_4–11 [pGlu⁵]-SP_5–11 and [pGlu⁶]SP_6–11 both at 400 and at 500 MHz. A spectral simulation was carried out on two of these peptides and the coupling constants were interpreted in terms of the conformations. The J_NH-CHa coupling constants are all ～8 Hz, with the exception of glycine, indicating no preferred conformation for the backbone. For the amino acids other than p-Glu, a comparison of the coupling constant data suggests the same relative rotamer populations for the side chains. Proton longitudinal relaxation time data were measured for all three peptides and support the above conclusions.     

A GHF7 CELLULASE FROM THE PROTIST SYMBIONT COMMUNITY OF Reticulitermes flavipes ENABLES MORE EFFICIENT LIGNOCELLULOSE PROCESSING BY HOST ENZYMES

Termites and their gut microbial symbionts efficiently degrade lignocellulose into fermentable monosaccharides. This study examined three glycosyl hydrolase family 7 (GHF7) cellulases from protist symbionts of the termite Reticulitermes flavipes. We tested the hypotheses that three GHF7 cellulases (GHF7‐3, GHF7‐5, and GHF7‐6) can function synergistically with three host digestive enzymes and a fungal cellulase preparation. Full‐length cDNA sequences of the three GHF7s were assembled and their protist origins confirmed through a combination of quantitative PCR and cellobiohydrolase (CBH) activity assays. Recombinant versions of the three GHF7s were generated using a baculovirus‐insect expression system and their activity toward several model substrates compared with and without metallic cofactors. GHF7‐3 was the most active of the three cellulases; it exhibited a combination of CBH, endoglucanase (EGase), and β‐glucosidase activities that were optimal around pH 7 and 30°C, and enhanced by calcium chloride and zinc sulfate. Lignocellulose saccharification assays were then done using various combinations of the three GHF7s along with a host EGase (Cell‐1), beta‐glucosidase (β‐glu), and laccase (LacA). GHF7‐3 was the only GHF7 to enhance glucose release by Cell‐1 and β‐glu. Finally, GHF7‐3, Cell‐1, and β‐glu were individually tested with a commercial fungal cellulase preparation in lignocellulose saccharification assays, but only β‐glu appreciably enhanced glucose release. Our hypothesis that protist GHF7 cellulases are capable of synergistic interactions with host termite digestive enzymes is supported only in the case of GHF7‐3. These findings suggest that not all protist cellulases will enhance saccharification by cocktails of other termite or fungal lignocellulases.     

Conformational Analysis of the Type II and Type III Collagen α-1 Chain C-Telopeptides by 1H NMR and Circular Dichroism Spectroscopy

Abstract

The type II and type III collagen α-1 chain C-telopeptides are a 27 mer with the sequence NAc- GPGIDMSAFAGLGPREKGPDPLQYMRA and a 22mer, NAc-GGGVASLGAGEKGPVG- YGYEYR, respectively. Their conformations have been studied in CD₃OH/H₂O (80/20) solution by means of two-dimensional proton NMR and CD spectroscopy. Based on TOCSY and NOESY experiments, all resonances were assigned and the conformational properties were analyzed in terms of vicinal NH-H_α coupling constants, sequential and medium range NOEs and amide proton temperature coefficients.

The conformation of the type II C-telopeptide is essentially extended. Evidence from CD spectroscopy suggests that a very minor proportion of the peptide might be helical (ca. 8%), but the NMR data show no evidence for a non-linear structure. The observation of reduced amide proton temperature dependence coefficients in certain sections of the molecule can, in view of the absence of any other supporting evidence, only be interpreted in terms of local shielding from solvent for sterical reasons (large hydrophobic side-chains).

The conformation of the type III C-telopeptide is mostly extended except for a β-turn ranging from Gly⁸ to Glu¹¹, which is stabilized by a hydrogen-bond between NH of Glu¹¹ and the carbonyl group of Gly⁸. The low temperature coefficient of NH(Glu¹¹) and, in particular, the observation of a medium range NOE between H_α (A⁹) and NH(E¹¹) corroborate the existence of a β-turn in this region. Although spectral overlap prevents a precise conclusion with regard to the type of β-turn present, there is some evidence that it might be type II.     

Subunit Secondary Structure in Filamentous Viruses: Predictions and Observations

Abstract

The algorithm of Gamier, Osguthorpe and Robson (J. Mol. Biol. 120, 97–120, 1978) for prediction of protein secondary structure has been applied to the coat protein sequences of six filamentous bacteriophages: fd, Ifl, IKe, Pfl, Xf and Pf3. For subunits of Class I virions (fd, Ifl, IKe), the algorithm predicts a very high percentage of helix in comparison to other structure types, which is in accord with the results of laser Raman and circular dichroism measurements. For subunits of the Class II virions (Pfl, Xf, Pf3), the algorithm consistently predicts a predominance of β structure, which is compatible with the demonstrated facility for conversion of Class II subunits from α-helix to β-strand under appropriate experimental conditions (Thomas, Prescott and Day, J. Mol. Biol. 165, 321–356, 1983). Even when the algorithm is biased to favor helix, the Class II virion subunits are predicted to contain considerably more strand than helix. Qualitatively similar results are obtained using the algorithm of Chou and Fasman {Adv. Enzym. 47, 45–148,45-148). Therefore, both predictive and experimental methods indicate a distinction between Gass I and II subunits, which is reflected in a greater tendency of the latter to adopt other than uniform β-helical conformation. The results suggest a possible model for the disassembly of filamentous viruses which may involve the unraveling of coat protein helices at the N terminus.