Highly organized structure in the non-coding region of the psbA minicircle from clade C Symbiodinium

The chloroplast genes of dinoflagellates are distributed among small, circular dsDNA molecules termed minicircles. In this paper, we describe the structure of the non-coding region of the psbA minicircle from Symbiodinium. DNA sequence was obtained from five Symbiodinium strains obtained from four different coral host species (Goniopora tenuidens, Heliofungia actiniformis, Leptastrea purpurea and Pocillopora damicornis), which had previously been determined to be closely related using LSU rDNA region D1/D2 sequence analysis. Eight distinct sequence blocks, consisting of four conserved cores interspersed with two metastable regions and flanked by two variable regions, occurred at similar positions in all strains. Inverted repeats (IRs) occurred in tandem or 'twin' formation within two of the four cores. The metastable regions also consisted of twin IRs and had modular behaviour, being either fully present or completely absent in the different strains. These twin IRs are similar in sequence to double-hairpin elements (DHEs) found in the mitochondrial genomes of some fungi, and may be mobile elements or may serve a functional role in recombination or replication. Within the central unit (consisting of the cores plus the metastable regions), all IRs contained perfect sequence inverses, implying they are highly evolved. IRs were also present outside the central unit but these were imperfect and possessed by individual strains only. A central adenine-rich sequence most closely resembled one in the centre of the non-coding part of Amphidinium operculatum minicircles, and is a potential origin of replication. Sequence polymorphism was extremely high in the variable regions, suggesting that these regions may be useful for distinguishing strains that cannot be differentiated using molecular markers currently available for Symbiodinium.

Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms

The central dogma of biology holds that genetic information normally flows from DNA to RNA to protein. As a consequence it has been generally assumed that genes generally code for proteins, and that proteins fulfil not only most structural and catalytic but also most regulatory functions, in all cells, from microbes to mammals. However, the latter may not be the case in complex organisms. A number of startling observations about the extent of non-protein-coding RNA (ncRNA) transcription in the higher eukaryotes and the range of genetic and epigenetic phenomena that are RNA-directed suggests that the traditional view of the structure of genetic regulatory systems in animals and plants may be incorrect. ncRNA dominates the genomic output of the higher organisms and has been shown to control chromosome architecture, mRNA turnover and the developmental timing of protein expression, and may also regulate transcription and alternative splicing. This paper re-examines the available evidence and suggests a new framework for considering and understanding the genomic programming of biological complexity, autopoletic development and phenotypic variation. BioEssays 25:930-939,2003. (C) 2003 Wiley Periodicals, Inc.

Electronic structure methods applied to gas-carbon reactions

A review is given on the fundamental studies of gas-carbon reactions using electronic structure methods in the last several decades. The three types of electronic structure methods including semi-empirical, ab initio and density functional theory, methods are briefly introduced first, followed by the studies on carbon reactions with hydrogen and oxygen-containing gases (non-catalysed and catalysed). The problems yet to solve and possible promising directions are discussed. (C) 2002 Elsevier Science Ltd. All rights reserved.

The 2.2 A crystal structure of a pocilloporin pigment reveals a nonplanar chromophore conformation

Reef-building corals contain host pigments, termed pocilloporins, that function to regulate the light environment of their resident microalgae by acting as a photoprotectant in excessive sunlight. We have determined the crystal structure of an intensely blue, non-fluorescent pocilloporin to 2.2 Angstrom resolution and a genetically engineered fluorescent variant to 2.4 Angstrom resolution. The pocilloporin chromophore structure adopts a markedly different conformation in comparison with the DsRed chromophore, despite the chromophore sequences (Gin-Tyr-Gly) being identical; the tyrosine ring of the pocilloporin chromophore is noncoplanar and in the trans configuration. Furthermore, the fluorescent variant adopted a noncoplanar chromophore conformation. The data presented here demonstrates that the conformation of the chromophore is highly dependent on its immediate environment.

Enzymatic cyclization of a potent Bowman-Birk protease inhibitor, sunflower trypsin inhibitor-1, and solution structure of an acyclic precursor peptide

The most potent known naturally occurring Bowman-Birk inhibitor, sunflower trypsin inhibitor-1 (SFTI-1), is a bicyclic 14-amino acid peptide from sunflower seeds comprising one disulfide bond and a cyclic backbone. At present, little is known about the cyclization mechanism of SFTI-1. We show here that an acyclic permutant of SFTI-1 open at its scissile bond, SFTI-1[ 6,5], also functions as an inhibitor of trypsin and that it can be enzymatically backbone-cyclized by incubation with bovine beta-trypsin. The resulting ratio of cyclic SFTI-1 to SFTI1[6,5] is similar to9:1 regardless of whether trypsin is incubated with SFTI-1[ 6,5] or SFTI-1. Enzymatic resynthesis of the scissile bond to form cyclic SFTI-1 is a novel mechanism of cyclization of SFTI-1[ 6,5]. Such a reaction could potentially occur on a trypsin affinity column as used in the original isolation procedure of SFTI-1. We therefore extracted SFTI-1 from sunflower seeds without a trypsin purification step and confirmed that the backbone of SFTI-1 is indeed naturally cyclic. Structural studies on SFTI-1[ 6,5] revealed high heterogeneity, and multiple species of SFTI-1[ 6,5] were identified. The main species closely resembles the structure of cyclic SFTI-1 with the broken binding loop able to rotate between a cis/trans geometry of the I7-P8 bond with the cis conformer being similar to the canonical binding loop conformation. The non-reactive loop adopts a beta-hairpin structure as in cyclic wild-type SFTI-1. Another species exhibits an isoaspartate residue at position 14 and provides implications for possible in vivo cyclization mechanisms.

Adsorption of N-2, Ar, acetone, chloroform and acetone-chloroform mixture on carbon black in the framework of molecular layer structure theory (MLST)

Adsorption of pure nitrogen, argon, acetone, chloroform and acetone-chloroform mixture on graphitized thermal carbon black is considered at sub-critical conditions by means of molecular layer structure theory (MLST). In the present version of the MLST an adsorbed fluid is considered as a sequence of 2D molecular layers, whose Helmholtz free energies are obtained directly from the analysis of experimental adsorption isotherm of pure components. The interaction of the nearest layers is accounted for in the framework of mean field approximation. This approach allows quantitative correlating of experimental nitrogen and argon adsorption isotherm both in the monolayer region and in the range of multi-layer coverage up to 10 molecular layers. In the case of acetone and chloroform the approach also leads to excellent quantitative correlation of adsorption isotherms, while molecular approaches such as the non-local density functional theory (NLDFT) fail to describe those isotherms. We extend our new method to calculate the Helmholtz free energy of an adsorbed mixture using a simple mixing rule, and this allows us to predict mixture adsorption isotherms from pure component adsorption isotherms. The approach, which accounts for the difference in composition in different molecular layers, is tested against the experimental data of acetone-chloroform mixture (non-ideal mixture) adsorption on graphitized thermal carbon black at 50 degrees C. (C) 2005 Elsevier Ltd. All rights reserved.

Semisolid structure formation and semisolid casting

Semisolid metal forming has now been accepted as a viable technology for production of components with complex shape and high integrity. The advantages of semisolid metal forming can only be achieved when the feedstock material has a non-dendritic semisolid structure. A controlled nucleation method has been developed to produce such structures for semisolid forming. By controlling grain nucleation and growth, fine-grained and non-dendritic microstructures that are suitable for semisolid casting can be generated. The method was applied to hypoeutectic and hypereutectic Al-Si casting alloys, Al wrought alloys and a Mg alloy. Parameters such as pouring temperature, cooling rate and grain refiner addition were controlled to achieve copious nucleation, nuclei survival and dendritic growth suppression during solidification. The influences of the controlling parameters on the formation of semisolid structure were different for each of these alloy groups. The as-cast structures were then partially remelted and isothermally held. Semisolid structures were developed and followed by semisolid casting into a stepped die.

The 2.1 angstrom crystal structure of the far-red fluorescent protein HcRed: Inherent conformational flexibility of the chromophore

We have determined the crystal structure of HcRed, a far-red fluorescent protein isolated from Heteractis crispa, to 2.1 resolution. HcRed was observed to form a dimer, in contrast to the monomeric form of green fluorescent protein (GFP) or the tetrameric forms of the GFP-like proteins (eqFP611, Rtms5 and DsRed). Unlike the well-defined chromophore conformation observed in GFP and the GFP-like proteins, the HcRed chromophore was observed to be considerably mobile. Within the HcRed structure, the cyclic tripeptide chromophore, Glu64-Tyr65-Gly66, was observed to adopt both a cis coplanar and a tran. non-coplanar conformation. As a result of these two con formations, the hydroxyphenyl moiety of the chromophore makes distinct interactions within the interior of the b-can. These data together with a quantum chemical model of the chromophore, suggest the cis coplanar conformation to be consistent with the fluorescent properties of HcRed, and the trans non-coplanar conformation to be consistent with non-fluorescent properties of hcCP, the chromoprotein parent of HcRed. Moreover, within the GFP-like family, it appears that where conformational freedom is permissible then flexibility in the chromophore conformation is possible. 2005 Elsevier Ltd. All rights reserved.

Theory of strongly correlated electron systems. II. Including correlation effects into electronic structure calculations

We have previously shown that a division of the f-shell into two subsystems gives a better understanding of the cohesive properties as well the general behavior of lanthanide systems. In this article, we present numerical computations, using the suggested method. We show that the picture is consistent with most experimental data, e.g., the equilibrium volume and electronic structure in general. Compared with standard energy band calculations and calculations based on the self-interaction correction and LIDA + U, the f-(non-f)-mixing interaction is decreased by spectral weights of the many-body states of the f-ion. (c) 2005 Wiley Periodicals, Inc.

Infracommunity structure of parasites of Hemigymnus melapterus (Pisces : Labridae) from Lizard Island, Australia: The importance of habitat and parasite body size

This Study describes the community of all metazoan parasites from 14 individuals of thicklip wrasse, Hemigymnus melapterus, from Lizard Island, Australia. All fish were parasitized, and 4,649 parasite individuals were found. Twenty-six parasite species were identified although only 6 species were abundant and prevalent: gnathiid isopods, the copepod Hatschekia hemigymni, the digenean Callohelmis pichelinae, and 3 morphotypes of tetraphyllidean cestode larvae. We analyzed whether the body size and microhabitat of the parasites and size of the host affected understanding of the structure of the parasite community. We related the abundance, biovolume, and density of parasites with the host body size and analyzed the abundances and volumetric densities of some parasite species within microhabitats. Although the 2 most abundant species comprised 75% of all parasite individuals, 4 species, each in similar proportion, comprised 85% of the total biovolume. Although larger host individuals had higher richness, abundance, and biovolume of parasites than smaller individuals, overall parasite volumetric density actually decreased with the host body size. Moreover. parasites exhibited abundances and densities significantly different among microhabitats; some parasite species depended on the area available, whereas others selected a specific microhabitat. Parasite and habitat size exhibited interesting relationships that should be considered more frequently. Considerations of these parameters improve understanding of parasite community structure and how the parasites use their habitats.