Molecular characterization of a weak fibrinogen-clotting enzyme from Trimeresurus jerdonii venom

A fibrinogen-clotting enzyme designed as jerdonobin-II was isolated from the venom of Trimeresurus jerdonii. It differed in molecular weight and N-terminal sequence with the previously isolated jerdonobin, a thrombin-like enzyme from the same venom. The enzyme consists of a single polypeptide chain with molecular weights of 30,000 and 32,000 under non-reducing and reducing conditions, respectively. Jerdonobin-II showed weak fibrinogen clotting activity and its activity unit on fibrinogen was calculated to be less than one unit using human thrombin as standard. The precursor protein sequence of jerodonobin-II was deduced from cloned cDNA sequence. The sequence shows high similarity (identity = 89%) to TSV-PA, a specific plasminogen activator from venom of T stejnegeri. Despite of the sequence similarity, jerdonobin-II was found devoid of plasminogen activating effect. Sequence alignment analysis suggested that the replacement of Lys(239) in TSV-PA to Gln(239) in jerdonobin-II might play an important role on their plasminogen activating activity difference. (C) 2005 Elsevier Ltd. All rights reserved.

Study of inter species diversity and population structure by molecular genetic method in Iranian Artemia

Artemia is a small crustacean that adapted to live in brine water and has been seen in different brine water sources in Iran. Considering the importance of genetic studies manifest inter population differences in species, to estimate genetic structure, detect difference at molecular level and separate different Artemia populations of Iran, also study of phylogenic relationships among them, samples of Artemia were collected from nine region: Urmia lake in West Azerbaijan, Shoor and Inche-Borun lakes in Golestan, Hoze-Soltan and Namak lakes in Qom, Maharloo and Bakhteghan lakes in Fars, Nough pool in Kerman and Mighan pool in Markazi and DNA extracted by phenol-chloroform method. Primers designed on a ribosomal fragment (16s rRNA) of mt DNA sequence and PCR was done. Digestion of the 1566 bp segment PCR product by 10 restriction endonuclease (Alu I, EcoR I, Eco47 I, Hae III, Hind III, Hinf I, Mbo I, Msp I, Rsa I, TaqI) showed 25 different haplotypes: 9 in Urmia, 4 in Shoor and Inche- Borun, 1 in Namak and Hoze-Soltan, 3 in Mighan, 1 in Bakhtegan Maharlo, 3 in Maharloo and 4 in Nough. Measurement of haplotype and nucleotide diversity intra population and nucleotide diversity and divergence inter populations and evolutionary distance between haplotypes showed a high diversity in mitochondrial genome of Artemia in studied regions whose results are similar to those explained for highly geographic expansion organism. In addition, results showed considerable heterogeneity between different populations and there are enough evidences in haplotypic level for separation of studied samples and division of Iranian Artemia to seven populations including Urmia, Shoor and Inche-Borun, Hoze-Soltan and Namak, Maharloo, Bakhteghan, Nough and Mighan. Phylogenetic analysis of the 16S rRNA data set resulted strict consensus and neighbor joining distance trees, demonstrated that all samples were monophyletic and parthenogenetic form derivation from bisexual populations and genetically high resemblance to those of A. urmiana. Study of 270 specimens from different region showed the genus Artemia in Iran clustered into three clades including: 1- Shoor, Inche-Burun, Hoze-Soltan, Namak, Bakhtegan and Maharloo 2- Nough and Mighan 3- Urmia. Totally, obtained results indicated to ability of used techniques for study of inter species diversity, population structure, reveal of phylogenic relationship and dividing of different populations of Artemia in Iran.

Molecular analysis of silver crucian carp (Carassius auratus gibelio Bloch) clones by SCAR markers

Random amplified polymorphic DNA (RAPD) molecular markers specific for one, two or three clones have been identified from five gynogenetic clones of silver crucian carp (Carassius auratus gibelio Bloch) using RAPD markers developed earlier. In this study, three RAPD markers (RA1-PA, RA2-EF and RA4-D) produced by Opj-1, and two RAPD DNA fragments (RA3-PAD and RA5-D) produced by Opj-7, were selected for molecular cloning and sequencing. Sequence data indicated that there were identical 801-bp nucleotide sequences in the shared marker RA1-PA cloned respectively from clones P and A, and the shared marker RA2-EF (which was cloned from clones E and F), were also of identical 958-by nucleotide sequences. The nucleotide sequences of the shared marker RA3-PAD fragments were also similar for 1181 by among clones P, A and D. The specific fragment RA4-D was composed of 628 bp, and the fragment RA5-D from clone D contained 385 nucleotides. According to the nucleotide sequences, we designed and synthesized five pairs of sequence characterized amplified regions (SCAR) primers to identify the specific fragments in these gynogenetic clones of silver crucian carp. Only individuals from clones P and A amplified a specific band using a pair of SCI-PA primers synthesized according to the marker RA1-PA sequences, whereas no products were detected in individuals from clones D, E and F. The PCR products amplified using SC2-EF and SC3-PAD primers were as expected. Furthermore, the pair of SC4-D primers amplified specific bands only in individuals from clone D, although weak bands could be produced in all individuals of the five clones when lower annealing temperatures were used. However, an additional pair of SC5-D primers designed from the RA5-D marker sequences could amplify a DNA band in individuals from clones P, A and D, and the same weak band was produced in clone E, whereas no products were detected in individuals from clone F. Searches in GenBank revealed that the 385-bp DNA fragment from RA5-D was homologous to the 5' end of gonadotropin I beta subunit 2 gene and growth hormone gene. No homologous sequences were found for other markers in GenBank. The SCAR markers identified in this study will offer a powerful, easy, and rapid method for discrimination of different clones and for genetic analyses that examine their origins and unique reproductive modes in crucian carp. Furthermore, they will likely benefit future selective breeding programs as reliable and reproducible molecular markers. (C) 2001 Elsevier Science B.V. All rights reserved.

Dispersion-compensating photonic crystal fibers with special characteristics

Based on the modified dual core structure, three kinds of special photonic crystal fibers are presented, which are extremely large negative dispersion, super-broad bond, and large area made field dispersion-compensating photonic crystal fibers (DCPCF). For extremely large negative dispersion DCPCF, the peak of negative dispersion reaches -5.9 x 10(4) ps/(mn km). Super-broad bond DCPCF has broadband large negative dispersion and the dispersion value varies linearly from -380 ps/(nm km) to -420 ps/(nm km) in the C band. The designed large area made field DCPCF has a peak dispersion of -1203 ps/(nm km) with the inner core mode area of 47 mu m(2) and outer core mode area of 835 mu m(2). Furthermore, for the large area mode field DCPCF, the experimental result is also obtained. (C) 2008 Wiley Periodicals, Inc.

Doping during low-temperature growth of materials for n-p-n Si/SiGe/Si heterojuction bipolar transistor by gas source molecular beam epitaxy

In situ doping for growth of n-p-n Si/SiGe/Si heterojuction bipolar transistor (HBT) structural materials in Si gas source molecular beam epitaxy is investigated. We studied high n-type doping kinetics in Si growth using disilane and phosphine, and p-type doping in SiGe growth using disilane, soild-Ge, and diborane with an emphasis on the effect of Ge on B incorporation. Based on these results, in situ growth of n-p-n Si/SiGe/Si HBT device structure is demonstrated with designed structural and carrier profiles, as verified from characterizations by X-ray diffraction, and spreading resistance profiling analysis. (C) 2000 Elsevier Science B.V. All rights reserved.

Effects of molecular structures on the olfactory responses of phospholipid membranes to four alcohols

In order to understand the relationship between phospholipid molecular structures and their olfactory responses to odorants, we designed and synthesized four phosphatidylcholine analogues with different long hydrocarbon (CH) chains and selected three natural phospholipids with different head-groups. By using interdigital electrodes (IEs) as olfactory sensors (OSs), we measured the responses of the Ifs coated with these seven different lipid membranes to four alcohol vapors in a gas flow system. The Ifs voltage changes were recorded and the voltage-relative saturate vapor pressure (V-P/P degrees) curves were also plotted. It was found that with a methyl (-CH3) placed at the C-8 position in the 18-carbon chain, the olfactory responses could be improved about ten times and with conjugated double bonds (C=C) in the long chains, the sensitivity could be increased by 3 similar to 4 orders of magnitude. As to head-groups, choline is preferred over ethanolamine and serine in phospholipid structures in terms of high olfactory sensitivity: These results are expected to be useful in further designing and manufacturing lipid-mimicking OSs. (C) 1998 Elsevier Science Ireland Ltd. All rights reserved.

Two-dimensional photonic crystals with a large photonic band gap designed by a rapid genetic algorithm

We used Plane Wave Expansion Method and a Rapid Genetic Algorithm to design two-dimensional photonic crystals with a large absolute band gap. A filling fraction controlling operator and Fourier transform data storage mechanism had been integrated into the genetic operators to get desired photonic crystals effectively and efficiently. Starting from randomly generated photonic crystals, the proposed RGA evolved toward the best objectives and yielded a square lattice photonic crystal with the band gap (defined as the gap to mid-gap ratio) as large as 13.25%. Furthermore, the evolutionary objective was modified and resulted in a satisfactory PC for better application to slab system.

The investigation of exfoliation process of organic modified montmorillonite in thermoplastic polyurethane with different molecular weights

Cloisite 30B (30B) was melt-mixed with two kinds of thermoplastic polyurethane (TPU) with different molecular weights to discern the roles of molecular diffusion and shear in the exfoliation process. The higher level of exfoliation was achieved in TPU matrix with higher molecular weight due to the appropriate viscosity. In order to have an insight into the mechanism of exfoliation, the degree of dispersion and exfoliation of 30B was characterized by wide angle X-ray diffraction and transmission electron microscopy. The layers of 30B were exfoliated via a slippage process, which was also observed in polyamide 12 nanocomposites recently.

Double propagation based on diepoxide, a facile route to high molecular weight poly(propylene carbonate)

Poly(propylene carbonate) (PPC) with number average molecular weight (M-n) higher than 200 kg/mol was prepared via the terpolymerization of carbon dioxide, propylene oxide and diepoxide using Y(CCl3OO)(3)-ZnEt2-glycerine coordination catalyst. When equimolar ZnEt2 and diepoxide were used, double propagation active species were generated in situ by nucleophilic attack of metal alkoxide on diepoxide, leading to PPC of doubled M-n value. The molecular weight of PPC has dramatic influence on its thermal and mechanical performances. PPC with M of 227 kg/mol showed modulus of 6900 MPa, while the modulus of PPC with M-n of 109 kg/mol was only 4300 MPa. Moreover, when M-n increased from 109 to 227 kg/mol, a 37 degrees C increase of the onset degradation temperature was observed.

Dispersion copolymerization of acrylamide with quaternary ammonium cationic monomer in aqueous salts solution

Dispersion copolymerization of acrylamide (AM) with 2-methylacryloylxyethyl trimethyl ammonium chloride (DMC) has been carried out in aqueous salts solution containing ammonium sulfate and sodium chloride with poly(acryloylxyethyl trimethyl ammonium chloride) (PDAC) as the stabilizer and 2,2'-azobis[2-(2-inidazolin-2-yl)propane]-dihydro chloride (VA-044) as the initiator. A new particle formation mechanism of the dispersion polymerization for the present system has been proposed. The effects of inorganic salts and stabilizer concentration on dispersion polymerization have been investigated. The results show that varying the salt concentration could affect the morphology and molecular weight of the resultant copolymer particles significantly. With increasing the stabilizer concentration, the particle size decreased at first and then increased, meanwhile the effect on the copolymer molecular weight was the contrary. These results had been rationalized based on the proposed mechanism.

Enhanced efficiency of light-emitting polymers through intra-molecular energy transfer

To enhance the photoluminescence and electroluminescence efficiency, light-emitting polymers with energy transferring chromophores including N,N,N'N'-phenylene-diamine, naphthalene-imide, oxadiazole, meta-phenylene vinylene are designed and synthesized.

Identification of Porphyra lines (Rhodophyta) by AFLP DNA fingerprinting and molecular markers

Twenty-seven Porphyra lines from 5 classes, including lines widely used in China, wild lines, and lines introduced to China from abroad in recent years, were screened by means of amplified fragment length polymorphism (AFLP) with 24 primer pairs. From the generated AFLP products, 13 bands that showed stable and repeatable AFLP patterns amplified by primer pairs M-CGA/E-AA and M-CGA/E-TA were scored and used to develop the DNA fingerprints of the 27 Porphyra lines. Moreover, the DNA fingerprinting patterns were converted into computer language expressed with digitals 1 and 0, which represented the presence (numbered as 1) or absence (numbered as 0) of the corresponding band. On the basis of these results, computerized AFLP DNA fingerprints were constructed in which each of the 27 Porphyra lines has its unique AFLP,fingerprinting pattern and can be easily distinguished from others. Software called PGI-AFLP (Porphyra germplasm identification-AFLP) was designed for identification of the 27 Porphyra lines. In addition, 21 specific AFLP markers from 15 Porphyra lines were identified; 6 AFLP markers from 4 Porphyra lines were sequenced, and 2 of them were successfully converted into SCAR (sequence characterized amplification region) markers. The developed AFLP DNA fingerprinting and specific molecular markers provide useful ways for the identification, classification, and resource protection of the Porphyra lines.

Identification of 27 Porphyra lines (Rhodophyta) by DNA fingerprinting and molecular markers

Twenty-seven Porphyra lines, including lines widely used in China, wild lines and lines introduced to China from abroad in recent years, were screened by random amplified polymorphic DNA (RAPD) technique with 120 operon primers. From the generated RAPD products, 11 bands that showed stable and repeatable RAPD patterns amplified by OPC-04, OPJ-18 and OPX-06, respectively were scored and used to develop the DNA fingerprints of the 27 Porphyra lines. Moreover, the DNA fingerprinting patterns were converted into computer language expressed with two digitals, 1 and 0, which represented the presence (numbered as 1) or absence (numbered as 0) of the corresponding band, respectively. Based on the above results, computerized DNA fingerprints were constructed in which each of the 27 Porphyra lines has its unique fingerprinting pattern and can be easily distinguished from others. Software named PGI (Porphyra germplasm identification) was designed for identification of the 27 Porphyra lines. In addition, seven specific RAPD markers from seven Porphyra lines were identified and two of them were successfully converted into SCAR (sequence characterized amplification region) markers. The developed DNA fingerprinting and specific molecular markers provide useful ways for the identification, classification and resource protection of the Porphyra lines.

Molecular cloning and expression of interleukin 1beta (IL-1 beta) from red seabream (Pagrus major)

The interleukin 1beta (IL-1beta) cDNA was cloned from the red seabream (Pagrus major) by homology cloning strategy. A cDNA fragment was amplified by PCR using two degenerated primers, which were designed according to the conserved regions of other known IL-1beta sequences, and elongated by 3' ends and 5' ends RACE PCR to get the full length coding sequence of red seabream IL-1beta (RS IL-1beta). The sequence contained 1252 nucleotides that included a 5' untranslated region (UTR) of 84 bp, a 3' UTR of 410 bp and an open reading frame (ORF) of 759 nucleotides which could be translated into a putative peptide of 253 amino acids with molecular weight of 28.6 kD and putative isoelectric point pI of 5.29. The deduced peptide contained two potential N-glycosylation sites and an identifiable IL1 family signature, but lacked the signal peptide and the clear ICE cut site, which were common in other nonmammalian IL-1beta genes. The RS IL-1beta had the highest homology with piscine IL-1beta according to phylogenetic tree analysis. The transcript expression was detected in blood, brain, gill, heart, head kidney, kidney, liver, muscle and spleen in the pathogen challenged and healthy red seabream by RTPCR. Results showed that the RS IL-1beta mRNA was constitutively expressed in most of the tissues both in stimulated and un-stimulated fish, and the expression could be enhanced by pathogen challenging.

Molecular identification of 16 Porphyra lines using sequence-related amplified polymorphism markers

Sequence-related amplified polymorphism (SRAP) is a novel molecular marker technique designed to amplify open reading frames (ORFs). The SRAP analytic system was set up and applied to Porphyra germplasm identification in this study for the first time. Sixteen Porphyra lines were screened by SRAP technique with 30 primer combinations. In the analysis, 14 primer combinations produced stable and reproducible amplification patterns in three repetitive experiments. Among the total 533 amplified fragments, 522 (98%) were polymorphic, with an average of 38 fragments for each primer combination, ranging in size from 50 to 500 bp. The 533 fragments were visually scored one by one and then used to develop a dendrogram with Unweighted Pair-Group Method Arithmetic Average (UPGMA), and the 16 Porphyra lines were divided into two major groups at the 0.68 similarity level. From the total 533 fragments, I I amplified by two primer combinations, ME1/EM1 and ME4/EM6, were used to develop the DNA fingerprints of the 16 Porphyra lines. The DNA fingerprints were then converted into binary codes, with I and 0 representing presence and absence of the corresponding amplified fragment, respectively. In the DNA fingerprints, each of the 16 Porphyra lines has its unique binary code and can be easily distinguished from the others. This is the first report on the development of SRAP technique and its utilization in germplasm identification of seaweeds. The results demonstrated that SRAP is a simple, stable, polymorphic and reproducible molecular marker technique for the classification and identification of Porphyra lines. (c) 2007 Elsevier B.V. All rights reserved.