Rapid evolution in a pair of recent duplicate segments of rice

Gene duplication has been considered the most important way of generating genetic novelties. The subsequent evolution right after gene duplication is critical for new function to occur. Here we analyzed the evolutionary pattern for a recently duplicated s

Phylogeographic differentiation of mitochondrial DNA in Han Chinese

To characterize the mitochondrial DNA (mtDNA) variation in Han Chinese from several provinces of China, we have sequenced the two hypervariable segments of the control region and the segment spanning nucleotide positions 10171-10659 of the coding region,

SCALING OF LIMB PROPORTIONS AND LIMB BONE DIAMETERS IN 3 SPECIES OF CHINESE SNUB-NOSED LANGURS (GENUS RHINOPITHECUS)

In this study, aspects of the structural mechanics of the upper and lower limbs of the three Chinese species of Rhinopithecus were examined. Linear regression and reduced major axis (RMA) analyses of natural log-transformed data were used to examine the dimensions of limb bones and other relationships to body size and locomotion. The results of this study suggest that: (1) the allometry exponents of the lengths of long limbs deviate from isometry, being moderately negative, while the shaft diameters (both sagittal and transverse) show significantly positive allometry; (2) the sagittal diameters of the tibia and ulna show extremely significantly positive allometry - the relative enlargement of the sagittal, as opposed to transverse, diameters of these bones suggests that the distal segments of the fore- and hindlimbs of Rhinopithecus experience high bending stresses during locomotion; (3) observations of Rhinopithecus species in the field indicate that all species engage in energetic leaping during arboreal locomotion. The limbs experience rapid and dramatic decelerations upon completion of a leap. We suggest that these occasional decelerations produce high bending stresses in the distal limb segments and so account for the hypertrophy of the sagittal diameters of the ulna and tibia.

Phylogenetic analysis of the family Thermaceae with an emphasis on signature position and secondary structure of 16S rRNA

The sequences of the 16S rRNA genes from 38 strains of the family Thermaceae were compared by alignment analysis. The genus-specific and species-specific base substitutions or base deletions (signature positions) were found in three hypervariable regions (in the helices 6, 10 and 17). The differentiation of secondary structures of the high variable regions in the 5' end (38-497) containing several signature positions further supported the concept. Based on the comparisons of the secondary structures in the segments of 16S rRNAs, a key to the species of the family Thermaceae was proposed. (C) 2003 Published by Elsevier Science B.V. on behalf of the Federation of European Microbiological Societies.

Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

Genetic divergence between Cyprinus carpio carpio and Cyprinus carpio haematopterus as assessed by mitochondrial DNA analysis, with emphasis on origin of European domestic carp

Although common carp is the major fish species in Asian and European aquaculture and many domestic varieties have occurred, there is a controversy about the origination of European domestic common carp. Some scientists affirmed that the ancestor of European domestic common carp was Danube River wild common carp, but others considered it might be Asian common carp. For elucidating origination of European domestic common carp, we chose two representative European domestic common carp strains (German mirror carp and Russian scattered scaled mirror carp) and one wild common carp strain of Cyprinus carpio carpio subspecies (Volga River wild common carp) and two Asian common carp strains, the Yangtze River wild common carp (Cyprinus carpio haematopterus) and traditionally domestic Xingguo red common carp, as experimental materials. ND5-ND6 and D-loop segments of mitochondrial DNA were amplified by polymerase chain reaction and analyzed through restriction fragment length polymorphism (RFLP) and sequencing respectively. The results revealed that HaeIII and DdeI digestion patterns of ND5-ND6 segment and sequences of control region were different between European subspecies C. carpio carpio and Asian subspecies C. carpio haematopterus. Phylogenetic analysis showed that German mirror carp and Russian scattered scaled mirror carp belonged to two subspecies, C. carpio carpio and C. carpio haematopterus, respectively. Therefore, there were different ancestors for domestic carp in Europe: German mirror carp was domesticated from European subspecies C. carpio carpio and Russian scattered scaled mirror carp originated from Asian subspecies C. carpio haematopterus.

Characterisation of a pathogenic virus isolated from marine threadfin fish (Eleutheronema tetradactylus) during a disease outbreak

An unknown virus was isolated from massive mortality of cultured threadfin (Eleutheronema tetradactylus) fingerlings. The virus replicated in BF-2 fish cell line and produced a plaque-like cytopathic effect. Electron micrographs revealed non-enveloped, icosahedral particles approximately 70-80 nm in diameter composed of a double capsid layer. Viroplasms and subviral particles approximately 30 run in diameter and complete particles of 70 nm in diameter were also observed in the infected BF-2 tissue culture cells. The virus was resistant upon pH 3 to 11 and ether treatment. It is also stable to heat treatment (3 h at 56 T). Replication was not inhibited by 5-iododeoxyuridine (5-IUdR). Acridine orange stain revealed typical reovirus-like cytoplasmic inclusion bodies. Electrophoresis of purified virus revealed 11 segments of double-stranded RNA and five major structural polypeptides of approximately 136, 132, 71, 41 and 33 kDa. Based on these findings, the virus isolated was identified to belong to the genus Aquareovirus and was designated as threadfin reovirus. This virus differed from a majority of other aquareovirus by its increase in virus infectivity upon exposure to various treatments such as high and low pH, heat (56 degreesC), ether and 5-IUdR. The RNA and virion protein banding pattern of the threadfin reovirus was shown to differ from another Asian isolate, the grass carp hemorrhage reovirus (GCV). Artificial injection of the threadfin reovirus into threadfin fingerlings resulted in complete mortality, whereas sea bass (Lates calcarifer) fingerlings infected via bath route showed severe mortality within a week after exposure. These results indicate that the threadfin virus is another pathogenic Asian aquareovirus isolate that could cross-infect into another marine fish, the sea bass. (C) 2002 Elsevier Science B.V. All rights reserved.

Common evolutionary origin of aquareoviruses and orthoreoviruses revealed by genome characterization of Golden shiner reovirus, Grass carp reovirus, Striped bass reovirus and golden ide reovirus (genus Aquareovirus, family Reoviridae)

Full-length and partial genome sequences of four members of the genus Aquareovirus, family Reoviridae (Golden shiner reovirus, Grass carp reovirus, Striped bass reovirus and golden ide reovirus) were characterized. Based on sequence comparison, the unclassified Grass carp reovirus was shown to be a member of the species Aquareovirus C The status of golden ide reovirus, another unclassified aquareovirus, was also examined. Sequence analysis showed that it did not belong to the species Aquareovirus A or C, but assessment of its relationship to the species Aquareovirus B, D, E and F was hampered by the absence of genetic data from these species. In agreement with previous reports of ultrastructural resemblance between aquareoviruses and orthoreoviruses, genetic analysis revealed homology in the genes of the two groups. This homology concerned eight of the 11 segments of the aquareovirus genome (amino acid identity 17-42%), and similar genetic organization was observed in two other segments. The conserved terminal sequences in the genomes of members of the two groups were also similar. These data are undoubtedly an indication of the common evolutionary origin of these viruses. This clear genetic relatedness between members of distinct genera is unique within the family Reoviridae. Such a genetic relationship is usually observed between members of a single genus. However, the current taxonomic classification of aquareoviruses and orthoreoviruses in two different genera is supported by a number of characteristics, including their distinct G+C contents, unequal numbers of genome segments, absence of an antigenic relationship, different cytopathic effects and specific econiches.

Complete nucleotide sequence of the S10 genome segment of grass carp reovirus (GCRV)

Hemorrhagic disease, caused by the grass carp reovirus (GCRV), is one of the major diseases of grass carp in China. Little is known about the structure and function of the gene segments of this reovirus. The S10 genome segment of GCRV was cloned and the complete nucleotide sequence is reported here. The S10 is 909 nucleotides long and contains a large open reading frame (ORF) encoding a protein of 276 amino acids with a deduced molecular weight of approximately 29.7 kDa. Comparisons of the deduced amino acid sequence of GCRV S10 with those of other reoviruses revealed no significant homologies. However, GCRV S10 shared a putative zinc-finger sequence and a similar distribution of hydrophilic motifs with the outer capsid proteins encoded by Coho salmon aquareovirus (SCSV) S10, striped bass reovirus (SBRV) S10, and mammalian reovirus (MRV) S4. It was predicted that this segment gene encodes an outer capsid protein.

Substitution Matrices of Residue Triplets Derived from Protein Blocks.

In protein sequence alignment, residue similarity is usually evaluated by substitution matrix, which scores all possible exchanges of one amino acid with another. Several matrices are widely used in sequence alignment, including PAM matrices derived from homologous sequence and BLOSUM matrices derived from aligned segments of BLOCKS. However, most matrices have not addressed the high-order residue-residue interactions that are vital to the bioproperties of protein.With consideration for the inherent correlation in residue triplet, we present a new scoring scheme for sequence alignment. Protein sequence is treated as overlapping and successive 3-residue segments. Two edge residues of a triplet are clustered into hydrophobic or polar categories, respectively. Protein sequence is then rewritten into triplet sequence with 2 · 20 · 2 = 80 alphabets. Using a traditional approach, we construct a new scoring scheme named TLESUMhp (TripLEt SUbstitution Matrices with hydropobic and polar information) for pairwise substitution of triplets, which characterizes the similarity of residue triplets. The applications of this matrix led to marked improvements in multiple sequence alignment and in searching structurally alike residue segments. The reason for the occurrence of the ‘‘twilight zone,’’ i.e., structure explosion of lowidentity sequences, is also discussed.

Controlled synthesis of 2D Au nanostructure assembly with the assistance of sulfonated polyaniline nanotubes

A wet chemical approach is used successfully to produce nanostructured Au material by the reduction of sulfonated polyaniline (SPANI) nanotubes. The Au nanostructures obtained are composed of single crystal Au nanoplates, which are aggregated layer-by-layer into stacks or edge-on-face into clusters at various conditions. The Au nanoplate diameter and thickness can be conveniently controlled in the range of 100 nm to 2 mu m and 10 to 30 nm, respectively, with no accompanying single Au nanoparticles being observed. The formation of the Au nanostructures was controlled by the degradation of SPANI. The gradually and slowly released segments of SPANI served as the reductant during the growth of the 2D Au nanostructures.

The influence of nucleating agent on crystallization behavior and properties of polypropylene and its copolymer with ethylene

The influences of nucleating agent EDBS on crystallization behavior and properties of polypropylene UP) and its copolymer with a small amount (4. 48 %, molar fraction) of ethylene (CPP) were studied. DSC results indicated that the crystallization temperature of iPP and CPP samples with 0.5 % (mass fraction) EDBS obviously increased and the degree of crystallinity of these samples became higher. In addition, adding small amount of EDBS enhanced the crystallization of the low isotacticity and low molecular weight segments of the CPP. PLM results showed that their spherulite size decreased markedly, and as a result, the transmittance and haze of the films were all improved.

Studies on blends of LLDPE and ethylene-methacrylic acid random copolymer

Blends of linear low-density polyethylene (LLDPE) and poly(ethylene-co-methacrylic acid) (EMA) random copolymer were studied by differential scanning calorimetry (DSC), wide-angle X-ray diffraction (WAXD), and excimer fluorescence. In binary blends, crystallization of EMA was studied, and no modification of crystal structure was detected. In excimer fluorescence measurements, emission intensities of blends of EMA and naphthalene-labeled LLDPE were measured. The ratio of the excimer emission intensity (I-D) to the emission intensity of the isolated "monomer" (I-M) decreases upon addition of EMA, indicating that PE segments of EMA interpenetrate into the amorphous phase of LLDPE. (C) 1998 Published by Elsevier Science Ltd,. All rights reserved.

Compatibilization effect of graft copolymer on immiscible polymer blends: 1. LLDPE/SBS/LLDPE-g-PS systems

compatibilizing effect of graft copolymer, linear low density polyethylene-g-polystyrene (LLDPE-g-PS), on immiscible blends of LLDPE with styrene-butadiene-styrene triblock copolymer (SBS) has been investigated by means of C-13 CPMAS n.m.r. and d.s.c. techniques. The results indicate that LLDPE-g-PS is an effective compatibilizer for LLDPE/SBS blends. It was found that LLDPE-g-PS chains connect two immiscible components, LLDPE and SBS, through solubilization of chemically identical segments of LLDPE-g-PS into the amorphous region of LLDPE acid PS block domain of SBS, respectively. It was also found that LLDPE-g-PS chains connect the crystalline region of LLDPE by isomorphism, with serious effects on the supermolecular structure of LLDPE. The effect of LLDPE-g-PS on the supermolecular structure of LLDPE in the LLDPE/SBS blends obviously depends on the composition of the blends, but has little dependence on the PS grafting yields of LLDPE-g-PS. (C) 1998 Elsevier Science Ltd. All rights reserved.

Compatibilization effect of graft copolymer on immiscible polymer blends .2. LLDPE/PS/LLDPE-g-PS systems

The compatibilizing effect of graft copolymer, linear low density polyethylene-g-polystyrene (LLDPE-g-PS), on immiscible LLDPE/PS blends has been studied by means of C-13 CP-MAS NMR and DSC techniques. The results indicate that LLDPE-g-PS is an effective compatibilizer for LLDPE/PS blends, and the compatibilizing effect of LLDPE-g-PS on LLDPE/PS blends depends on the PS grafting yield and molecular structure of the compatibilizers and also on the composition of the blends. It was found that LLDPE-g-PS chains connect two immiscible components, LLDPE and PS, through solubilization of chemically identical segments of LLDPE-g-PS into the noncrystalline region of the LLDPE and PS domain, respectively. Meanwhile, LLDPE-g-PS chains connect the crystalline region of LLDPE by isomorphism, resulting in an obvious change in the crystallization behavior of LLDPE. (C) 1996 John Wiley & Sons, Inc.