Cloning and characterization of cytochrome c oxidase subunit I (COXI) in Gobiocypris rarus

In study of gene expression profile in cloned embryos which derived from D. rerio embryonic nuclei and G. rarus enucleated eggs, cytochrome c oxidase subunit I (COXI) of G. rarus, exhibiting difference at expression level between cloned embryos and zebrafish embryo, was cloned. Its full cDNA length is 1654 bp and contains a 1551 bp open reading frame, encoding a 5.64 kDa protein of 516 amino acids. The alignment result shows that mitochondrion tRNA(ser) is co-transcripted with COXI, which just was the 3'-UTR of COXI. Molecular phylogenic analysis based on COXI indicates G. rarus should belong to Gobioninae, which was not in agreement with previous study according to morphological taxonomy. Comparison of DNA with cDNA shows that RNA editing phenomenon does not occur in the COXI of G. rarus.

Cloning and expression of medaka dazl during ernbryogenesis and gametogenesis

The Deleted in azoospermia family consists of RNA-binding proteins Bottle, Daz, and Daz-like (Dazl) that are expressed in the germline. Here, we report the cloning and expression of the medakafish (Oryzias latipes) dazl gene (odazl). Interestingly, although the predicted medaka Dazl protein (oDazl) contains a RRM motif and a DAZ repeat characteristic of its mammalian homologs, it lacks 80 aa at the C-terminus. By RT-PCR, RNA in situ hybridization, Western blotting and fluorescent immunohistochemistry using a rabbit anti-DazI antibody (alpha Oazl), we analyzed the expression patterns of odazl and its protein. The odazl transcript persists throughout embryogenesis and delineates with primordial germ cells. In adults, the expression of odazl RNA and its protein is restricted to germ cells of both the testis and ovary. We observed differential expression of RNA and protein at critical stages of gametogenesis. In the testis, the odazl RNA is low at premeiotic stages, abundant at meiotic stages, but absent in postmeiotic stages; whereas the oDazl protein is rich in premeiotic stages, reduced at meiotic stages, becomes barely detectable or absent in postmeiotic round spermatids or sperm, respectively. This is in sharp mature spermatozoa. In the ovary, the odazl RNA contrast to the human situation where the Dazl transcript and protein are present in and protein persist throughout oogenesis and also show differential expression at premeiotic, meiotic and postmeiotic stages. Thus, the odazl or its protein is a marker for germ cells during embryogenesis and at critical stages of gametogenesis in both sexes of medaka. (c) 2006 Elsevier B.V. All rights reserved.

Sox genes in grass carp (Ctenopharyngodon idella) with their implications for genome duplication and evolution

The Sox gene family is found in a broad range of animal taxa and encodes important gene regulatory proteins involved in a variety of developmental processes. We have obtained clones representing the HMG boxes of twelve Sox genes from grass carp (Ctenopharyngodon idella), one of the four major domestic carps in China. The cloned Sox genes belong to group B1, B2 and C. Our analyses show that whereas the human genome contains a single copy of Sox4, Sox11 and Sox14, each of these genes has two co-orthologs in grass carp, and the duplication of Sox4 and Sox11 occurred before the divergence of grass carp and zebrafish, which support the "fish-specific whole-genome duplication" theory. An estimation for the origin of grass carp based on the molecular clock using Sox1, Sox3 and Sox11 genes as markers indicates that grass carp (subfamily Leuciscinae) and zebrafish (subfamily Danioninae) diverged approximately 60 million years ago. The potential uses of Sox genes as markers in revealing the evolutionary history of grass carp are discussed.

Development of polymorphic EST markers in Penaeus monodon: applications in penaeid genetics

The objective of this study was to develop type I markers for genome mapping and other genetic studies of Penaeus monodon. Primers were designed based on expressed sequence tags (ESTs) from a P monodon cephalothorax cDNA library to amplify 100-300 bp products. 34 of the primer pairs successfully amplified PCR products from genomic DNA. Single-strand conformation polymorphism analysis showed that similar to 30% of the ESTs tested exhibit polymorphism in a test panel of P monodon individuals. Mendelian inheritance of the EST-derived markers has been established in two international reference mapping families of P monodon, and mapping of these markers is in progress. Some ESTs were successfully amplified from other Penaeus species (P. chinensis, P japonicus and P vannamei), indicating that the markers are applicable in cross-species comparison. Two populations of P. japonicus could be differentiated using one of the ESTS. In conclusion, the polymorphic EST markers developed in this study are applicable in genome mapping and population genetic studies of penaeid shrimp. (C) 2002 Elsevier Science B.V. All rights reserved.

Alleviation of pre-exposure of mouse brain with low-dose C-12(6+) ion or Co-60 gamma-ray on male reproductive endocrine damages induced by subsequent high-dose irradiation

Irradiation has been widely reported to damage organisms by attacking on proteins, nucleic acid and lipids in cells. However, radiation hormesis after low-dose irradiation has become the focus of research in radiobiology in recent years. To investigate the effects of pre-exposure of mouse brain with low-dose C-12(6+) ion or Co-60 gamma (gamma)-ray on male reproductive endocrine capacity induced by subsequent high-dose irradiation, the brains of the B6C3F(1) hybrid strain male mice were irradiated with 0.05 Gy of C-12(6+) ion or Co-60 gamma-ray as the pre-exposure dose, and were then irradiated with 2 Gy as challenging irradiation dose at 4 h after pre-exposure. Serum pituitary gonadotropin hormones, follicle-stimulating hormone (FSH) and luteinizing hormone (LH), testosterone, testis weight, sperm count and shape were measured on the 35th day after irradiation. The results showed that there was a significant reduction in the levels of serum FSH, LH, testosterone, testis weight and sperm count, and a significant increase in sperm abnormalities by irradiation of the mouse brain with 2 Gy of C-12(6+) ion or Co-60 gamma-ray. Moreover, the effects were more obvious in the group irradiated by C-12(6+) ion than in that irradiated by Co-60 gamma-ray. Pre-exposure with low-dose C-12(6+) ion or Co-60 gamma-ray significantly alleviated the harmful effects induced by a subsequent high-dose irradiation.

Deconfinement phase Transition including perturbative QCD corrections in (proto)neutron star matter

Deconfinement phase transition and neutrino trapping in (proto)neutron star matter are investigated in a chiral hadronic model (also referred to as the FST model) for the hadronic phase (HP) and in the color-flavor-locked (CFL) quark model for the deconfined quark phase. We include a perturbative QCD correction parameter alpha(s) in the CFL quark matter equation of states. It is shown that the CFL quark core with K-0 condensation forms in neutron star matter with the large value of alpha(s). If the small value of alpha(s) is taken, hyperons suppress the CFL quark phase and the HP is dominant in the high-density region of (proto)neutron star matter. Neutrino trapping makes the fraction of the CFL quark matter decrease compared with those without neutrino trapping. Moreover, increasing the QCD correction parameter alpha(s) or decreasing the bag constant B and the strange quark mass m(s) can make the fraction of the CFL quark matter increase, simultaneously, the fraction of neutrino in protoneutron star matter increases, too. The maximum masses and the corresponding radii of (proto)neutron stars are not sensitive to the QCD correction parameter alpha(s).

Pressurized electrochromatography coupled with electrospray ionization mass spectrometry for analysis of peptides and proteins

Pressurized capillary electrochromatography (pCEC) was coupled with electrospray ionization mass spectrometry (ESI-MS) using a coaxial sheath liquid interface. It was used for separation and analysis of peptides and proteins. The effects of organic modifier and applied voltage on separation were investigated, and the effects of pH value of the mobile phase and the concentration of the electrolyte on ESI-MS signal were investigated. The resolution and detection sensitivity with different separation methods (pCEC, capillary high-performance liquid chromatography) coupled on-line with mass spectrometry were compared for the separation of a peptide mixture. To evaluate the feasibility and reliability of the experimental setup of the system, tryptic digests of cytochrome c and modified protein as real samples were analyzed by using pCEC-ESI-MS.

Immobilized metal-ion chelating capillary microreactor for peptide mapping analysis of proteins by matrix assisted laser desorption/ionization-time of flight-mass spectrometry

Peptide mass mapping analysis, utilizing a regenerable enzyme microreactor with metal-ion chelated adsorption of enzyme, combined with matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) was developed. Different procedures from the conventional approaches were adopted to immobilize the chelator onto the silica supports, that is, the metal chelating agent of iminodiacetic acid (IDA) was reacted with glycidoxypropyltrimethoxysilane (GLYMO) before its immobilization onto the inner wall of the fused-silica capillary pretreated with NH4HF2. The metal ion of copper and subsequently enzyme was specifically adsorbed onto the surface to form the immobilized enzyme capillary microreactor, which was combined with MALDI-TOF-MS to apply for the mass mapping analysis of nL amounts of protein samples. The results revealed that the peptide mapping could routinely be generated from 0.5 pmol protein sample in 15 min at 50degreesC, even 20 fmol cytochrome c could be well digested and detected.

Affinity membrane chromatography for the analysis and purification of proteins

Affinity chromatography is unique among separation methods as it is the only technique that permits the purification of proteins based on biological functions rather than individual physical or chemical properties. The high specificity of affinity chromatography is due to the strong interaction between the ligand and the proteins of interest. Membrane separation allows the processing of a large amount of sample in a relatively short time owing to its structure, which provides a system with rapid reaction kinetics. The integration of membrane and affinity chromatography provides a number of advantages over traditional affinity chromatography with porous-bead packed columns, especially with regard to time and recovery of activity. This review gives detailed descriptions of materials used as membrane substrates, preparation of basic membranes, coupling of affinity ligands to membrane supports, and categories of affinity membrane cartridges. It also summarizes the applications of cellulose/glycidyl methacrylate composite membranes for proteins separation developed in our laboratory. (C) 2001 Elsevier Science B.V. All rights reserved.

Quantitative electrochemiluminescence detection of proteins: Avidin-based sensor and tris(2,2 '-bipyridine) ruthenium(II) label

Quantitative electrochemilumineseence (ECL) detection of a model protein, bovine serum albumin (BSA) was achieved via biotin-avidin interaction using an avidin-based sensor and a well-developed ECL system of tris(2,2'-bipyridine) ruthenium(II) derivative as label and tri-n-propylamine (TPA) as coreactant. To detect the protein, avidin was linked to the glassy carbon electrode through passive adsorptions and covalent interaction with carboxylate-terminated carbon nanotubes that was used as binder to immobilize avidin onto the electrode. Then, biotinylated BSA tagged with tris(2,2'-bipyridine) ruthenium(II) label was attached to the prepared avidin surface.

A bifunctional structure for the direct electron transfer of Cytochrome c

It was found that silicon dioxide (SiO2) nanoparticles modified onto glassy carbon (GC) electrode exhibited a dramatic promotion on the direct electron transfer of Cytochrome c (Cyt c). The corresponding mechanism was discussed based on the electrochemical characteristics and a spatial geometrical model of the bifunctional structure. The model could offer insight to the study of biosensors and bioreactors without chemical mediator and serve as a basis for their fabrication. (c) 2008 Elsevier Ltd. All rights reserved.

Water-soluble phosphate-functionalized polyfluorene as fluorescence biosensors toward cytochrome c

An anionic water-soluble polyfluorene derivative, poly(9,9-bis(6'-phosphatehexyl)fluorene-alt-1,4-phenylene) sodium salt (PFHPNa), was synthesized by Suzuki coupling reaction in DMF/water. Polymer PFHPNa was well soluble in water with a strong blue fluorescence emission. Effect of the side chain length on fluorescence sensory properties was studied by comparing quenching efficiencies toward different quenchers of PFHPNa with a reported polymer poly(9,9-bis(3'-phosphatepropyl)fluorene-alt-1,4-phenylene) sodium salt (PFPPNa), which have different side chains in length. For small molecular quenchers (methylviologen, MV2+) and meso-5,10,15,20-tetrakis-(N-methyl-4-pyridyl)porphine (TMPyP4), polymer PFHPNa had lower sensitivity due to the much longer side chain length. The positively charged metalloprotein cytochrome c could quench fluorescence of conjugated polymers via energy transfer and electron transfer.

Direct electrochemistry behavior of Cytochrome c on silicon dioxide nanoparticles-modified electrode

A newfangled direct electrochemistry behavior of Cytochrome c (Cyt c) was found on glassy carbon (GC) electrode modified with the silicon dioxide (SiO2) nanoparticles by physical adsorption. A pair of stable and well-defined redox peaks of Cyt c ' quasi-reversible electrochemical reaction were obtained with a heterogeneous electron transfer rate constant of 1.66 x 10(-3) cm/s and a formal potential of 0.069 V (vs. Ag/AgCl) (0.263 V versus NHE) in 0.1 mol/L pH 6.8 PBS. Both the size and the amount of SiO2 nanoparticles could influence the electron transfer between Cyt c and the electrode. Electrostatic interaction which is between the negative nanoparticle surface and positively charged amino acid residues on the Cyt c surface is of importance for the stability and reproducibility toward the direct electron transfer of Cyt c. It is suggested that the modification of SiO2 nanoparticles proposes a novel approach to realize the direct electrochemistry of proteins.

Surface-enhanced resonance Raman spectroscopy and spectroscopy study of redox-induced conformational equilibrium of cytochrome c adsorbed on DNA-modified metal electrode

The redox-induced conformational equilibrium of cytochrome c (cyt c) adsorbed on DNA-modified metal electrode and the interaction mechanism of DNA with cyt c have been studied by electrochemical, spectroscopic and spectroelectrochemical techniques. The results indicate that the external electric field induces potential-dependent coordination equilibrium of the adsorbed cyt c between its oxidized state (with native six-coordinate low-spin and non-native five-coordinate high-spin heme configuration) and its reduced state (with native six-coordinate low-spin heme configuration) on DNA-modified metal electrode. The strong interactions between DNA and cyt c induce the self-aggregation of cyt c adsorbed on DNA. The orientational distribution of cyt c adsorbed on DNA-modified metal electrode is potential-dependent, which results in the deviation from an ideal Nernstian behavior of the adsorbed cyt c at high electrode potentials. The electric-field-induced increase in the activation barrier of proton-transfer steps attributed to the rearrangement of the hydrogen bond network and the self-aggregation of cyt c upon adsorption on DNA-modified electrode strongly decrease the interfacial electron transfer rate.

Syntheses of fully sulfonated polyaniline nano-networks and its application to the direct electrochemistry of cytochrome c

Fully sulfonated polyaniline nano-particles, nano-fibrils and nano-networks have been achieved for the first time by electrochemical homopolymerization of orthanilic acid using a three-step electrochemical deposition procedure in a mixed solvent of acetonitrile (ACN) and water. The diameter of the uniform nano-particles is about 60nm, and the nano-fibrils can be organized in two-dimensional (21)) or three-dimensional (313) non-periodic networks with good electrical contact. Average distance between contacts is about 850 and 600 nm for a 2D and 3D system, respectively. The details of the poly(orthanilic acid) (POA) nano-structure were examined with a field emission scanning electron microscope (SEM). The structure and properties of POA were characterized with FTIR, UV-vis and electrochemical methods. The 3D POA nano-networks coated platinum electrode gave a direct electrochemical behavior of horse heart cytochrome c (Cyt c) immobilized on this electrode surface, a pair of well-defined redox waves with formal potential (E-ol) of -0.032 V (versus Ag/AgCl) was achieved. The interaction between Cyt c and POA makes the formal potential shift negatively compared to that of Cyt c in solution. Spectrophotometric and electrochemical methods were used to investigate the interaction of Cyt c with POA.