Identification of the sex of a wide range of Carinatae birds by PCR using primer sets selected from chicken EE0.6 and its related sequences

A 0.6 kb EcoRI fragment (EE0.6), cloned from the W chromosome of chickens, is a nonrepetitive sequence and contains an exonlike sequence, ET15, which is likely a part of a pseudogene. The EE0.6 sequence is conserved in all species of birds examined both in Carinatae and Ratitae. A counterpart sequence of EE0.6 is present on the Z chromosome. The extent of diversity between the W- and Z-linked sequences are variable among species. The W- and Z-linked EE0.6 sequences, cloned from 12 different species, were compared and four forward and three reverse primers were selected to amplify parts of the EE0.6 sequence by polymerase chain reaction (PCR). By choosing a suitable combination of primers for EE0.6 and a set of primers for a Z/W-common sequence, as an internal control, the sex of 36 species belonging to 16 different orders of Carinatae could be determined clearly by PCR. The sex of two other species representing different orders could be determined by Southern blot hybridization using ET15 as a probe. For the two Ratitae species, emu and ostrich, EE0.6 sequences on W and Z chromosomes could not be distinguished either by PCR or Southern blotting.     

Influence of end-to-end diffusion on intramolecular energy transfer as observed by frequency-domain fluorometry

We investigated the influence of end-to-end diffusion on intramolecular energy transfer between a naphthalene donor and dansyl acceptor linked by polymethylene chain. A range of viscosities from 0.6 to 200 cP were obtained using propylene glycol at different temperatures (0-80 degrees C) and methanol at 20 degrees C. The intensity decays of naphthalene were measured in the frequency domain. Several theoretical models, including distance distributions, were used to fit the data. The results indicate that end-to-end diffusion of flexible donor-acceptor pairs can be detected and quantified using frequency-domain fluorometry, even in the presence of a distribution of donor-to-acceptor distances.     

A new structural protein located in the Z lines of chicken skeletal muscle.

A new structural protein was purified from a prolonged 0.6 M KI extract of residues of chicken skeletal myofibrils, from which myosin, actin, and some other proteins had been removed. The protein had a chain weight of 55,000. The indirect immunofluorescence technique using antiserum against the 55,000 dalton protein revealed that the protein was exclusively located in the Z lines of a myofibril. The new protein formed lattice structures in vitro which were similar to those observed in the Z lines in situ.     

Triiodothyronine influences quail myoblast proliferation and differentiation*

The influence of triiodothyronine (T3) on avian myoblast proliferation and differentiation was studied in secondary cultures using plating densities of 2500 and 7000 cells/cm². Culture media were depleted of T3 (control myoblasts) and increasing amounts were then added to concentrations of 0.6, 3 and 15 nM T3 (treated myoblasts). Independent of the cell density, T3 induced a dose-related decrease in myoblast proliferation measured by cell number, doubling time and ³H-thymidine incorporation. However, with the lower plating density, this influence was delayed, occurring only after the third day of culture for 0.6 nM T3-treated myoblasts and simultaneous with the onset of myosin heavy chain accumulation. Moreover, when myoblasts were exposed to BrdU for 48 h, the T3 growth inhibitory effect disappeared, thus showing that this effect was clearly linked to differentiation. In addition, we have shown that T3 induced an early fusion of myoblasts: 65% of the maximal value of the fusion index was reached on day 3 in the T3-treated cells in comparison to 25% in the control myoblasts. This hormone also enhanced accumulation of muscle-specific proteins (connectin, acetylcholine receptors, myosin heavy chain), tested by cytoimmunofluorescence, ELISA, binding experiments and Western blot. All these results show that T3 increased myoblast differentiation through a pathway including myoblast withdrawal from the cell cycle. The influence of T3 could partly explain its previously reported positive effect on the number of muscle fibers.     

The effect of myosin phosphorylation on the contractile properties of skinned rabbit skeletal muscle fibers

We have studied the effect of myosin P-light chain phosphorylation on the isometric tension generated by skinned fibers from rabbit psoas muscle at 0.6 and 10 microM Ca2+. At the lower Ca2+ concentration, which produced 10-20% of the maximal isometric tension obtained at 10 microM Ca2+, addition of purified myosin light chain resulted in a 50% increase in isometric tension which correlated with an increase in P-light chain phosphorylation from 0.10 to 0.80 mol of phosphate/mol of P-light chain. Addition of a phosphoprotein phosphatase reversed the isometric tension response and dephosphorylated P-light chain. At the higher Ca2+ concentration, P-light chain phosphorylation was found to have little effect on isometric tension. Fibers prepared and stored at -20 degrees C in a buffer containing MgATP, KF, and potassium phosphate incorporated 0.80 mol of phosphate/mol of P-light chain. Addition of phosphoprotein phosphatase to these fibers incubated at 0.6 microM Ca2+ caused a reduction in isometric tension and dephosphorylation of the P-light chain. There was no difference before and after phosphorylation of P-light chain in the normalized force-velocity relationship for fibers at the lower Ca2+ concentration, and the extrapolated maximum shortening velocity was 2.2 fiber lengths/s. Our results suggest that in vertebrate skeletal muscle, P-light chain phosphorylation increases the force level at submaximal Ca2+ concentrations, probably by affecting the interaction between the myosin cross-bridge and the thin filament.     

Cross-linking of native myosin forms oligomers of myosin heavy chain dimers

Chemical cross-linking of native myosin in 0.6 M NaCl with p-phenylene bis maleimide or glutaraldehyde resulted in rapid formation of myosin heavy chain dimers and their oligomers. Monomers and odd-number oligomers disappeared after the prolonged treatment with these reagents. When denatured myosin was cross-linking, myosin heavy chain monomers and odd-number oligomers remained after the prolonged treatment, although dimers and their even-number oligomers were abundant. For high molecular weight markers, myosin heavy chain oligomers formed from denatured myosin with glutaraldehyde or p-phenylene bis maleimide are recommended.     

Effects of polyelectrolyte chain stiffness, charge mobility, and charge sequences on binding to proteins and micelles

The binding affinities of polyanions for bovine serum albumin in NaCl solutions from I = 0.01-0.6 M, were evaluated on the basis of the pH at the point of incipient binding, converting each such pH(c) value into a critical protein charge Zc. Analogous values of critical charge for mixed micelles were obtained as the cationic surfactant mole fraction Yc. The data were well fitted as Yc or Zc = KI a, and values of K and a were considered as a function of normalized polymer charge densities (tau), charge mobility, and chain stiffness. Binding increased with chain flexibility and charge mobility, as expected from simulations and theory. Complex effects of tau were related to intrapolyanion repulsions within micelle-bound loops (seen in the simulations) or negative protein domain-polyanion repulsions. The linearity of Zc with radicalI at I < 0.3 M was explained by using protein electrostatic images, showing that Zc at I < 0.3 M depends on a single positive "patch"; the appearance of multiple positive domains I > 0.3 M (lower pH(c)) disrupts this simple behavior.     

Comparison of the Unit-chain Distributions of Glycogens from Different Biological Sources,Revealed by Anion Exchange Chromatography

The precise distributions of α-1,4-unit-chains of several kinds of glycogens, average chain length 7–13, from different sources, e.g., mammals, shellfish, mushrooms, and microorganisms, were compared using high performance anion exchange chromatography (HPAEC). These glycogens were completely debranched, and a series of maltosaccharides derived from individual unit-chains were analyzed. Most glycogens had similar chromatographic profiles, with degrees of polymerization (DPs), from 4–5 to 35; oyster glycogen contained shorter chains of DP 2–3. On the other hand, molar-based distribution patterns of these glycogens appeared to be specific to their origins. Ratios of their A- to B-chains varied from 0.6: 1 to 1.2: 1, as estimated by quantitative HPAEC of maltosaccharides by debranching of the β-limit dextrins. Possible chain lengths of the exterior A-chains were also discussed.     

Frequent occurrence of CYP2D6*10 duplication allele in a Japanese population

Allele-specific long-polymerase chain reaction (PCR), PCR-restriction fragment length polymorphism (RFLP) and haplotype analysis using XbaI and EcoRI were used to determine whether gene duplication of CYP2D6*10 exists in a Japanese population of 162 healthy subjects. Based on the results of PCR and haplotype analysis, the frequencies of CYP2D6*1X2, CYP2D6*2X2 and CYP2D6*10X2 in the Japanese population were estimated to be 0.3, 0.3 and 0.6%, respectively. The results suggest that duplicated alleles of CYP2D6*10 exist in the Japanese population and that it may be one of the factors affecting the capacity of Japanese to metabolize various CYP2D6 substrate drugs.     

Goat immunoglobin G. Peptide chains and terminal residues

Goat immunoglobulin G (IgG) was isolated and characterized. The molecular weights of the IgG and its heavy chains and light chains were found to be 144000, 53600 and 23000 respectively. The light chain corresponds to human L type as was shown by the absence of C-terminal S-carboxymethylcysteine and its high content of N-terminal pyrrolid-2-one-5-carboxylic acid (PCA). The major C-terminal residue of the light chain was serine and the major N-terminal dipeptide was PCA-Ala (0.6mole/mole). The major C-terminal residue of the heavy chain was glycine and the N-terminal sequence of the heavy chain is PCA-Val-Gln. This tripeptide was obtained in a 70% yield.     

High-molecular-weight kininogen from horse plasma. Isolation, characterization and comparison with bovine high-Mr kininogen

High-molecular-weight (high-Mr) kininogen was purified from horse plasma by chromatography on columns of DEAE-Sephadex A-50, CM-Sephadex C-50, p-chlorobenzylamine-Sepharose and Sephadex G-150. The yield was about 150 mg from 81 of fresh plasma. The purified material gave a single band on sodium dodecylsulfate/polyacrylamide gel electrophoresis and a single precipitin line on immunodiffusion and immunoelectrophoresis. The molecular weight of horse high-Mr kininogen was estimated to be 78000 by dodecylsulfate gel electrophoresis using the Ferguson plot. Its polypeptide content was determined to be 86% by amino acid analysis and there was a total of 581 amino acid residues/molecule of protein. The kininogen contained a total of 13.9% carbohydrates, consisting of hexoses (7.8%), glucosamine (1.9%), galactosamine (0.6%) and sialic acid (3.6%). On incubation of horse high-Mr kininogen with bovine and horse plasma kallikreins, several fragments which contained extremely high levels of histidine, were liberated, in addition to kinin. After the liberation of kinin and histidine-rich fragments, a protein free of kinin and its fragments was isolated. This protein consisted of two polypeptide chains, heavy chain and light chain, which are bridged by disulfide bonds. The molecular weight and amino acid composition of the heavy chain and the light chain from horse high-Mr kininogen were very similar to those of the heavy and light chains from bovine high-Mr kininogen, respectively. From these results, it was revealed that horse high-Mr kininogen is quite similar to bovine high-Mr kininogen in terms of their physicochemical and chemical properties, although they are immunologically distinguishable.     

Quantification of plasma-derived blood coagulation factor VIII by real-time biosensor measurements

Plasma-derived blood coagulation factor VIII was analyzed in real time using biosensor technology. Monoclonal antibodies directed against the heavy and against the light chain of factor VIII were immobilized on different carboxymethyl dextran surfaces. Different factor VIII concentrations were injected over the antibody surfaces in parallel and response levels were determined from the dissociation phase at a fixed time after sample injection. Serial dilutions of plasma-derived factor VIII with known concentrations determined by a commercial FVIIIC:Ag ELISA were used as standards. A quantification limit of 0.9 I.U./ml with antibody 530p and 1.5 I.U./ml with antibody 531p was calculated. Intra-assay precision expressed as percent coefficient of variation was below 10% for concentrations above 0.6 I.U./ml. Inter-assay precision for antibody 530p was below 20% for concentrations higher than 0.6 I.U./ml. For 531p, inter-assay precision was below 10% for concentrations higher than 2 I.U./ml. A sensor chip lifetime in respect to regeneration of at least 100 cycles for both antibodies was found. The small sample requirement of 35 μl allows fast analysis of different FVIII products and the use of two monoclonal antibodies directed against two different FVIII domains provides additional information about the integrity of the FVIII molecule.     

Selection of RAPD marker for growth of seedlings at low temperature in rice.

We have developed a polymerase chain reaction (PCR)-based assay that could effectively reduce the time period required to screen and select the cold tolerance gene of rice seedlings under field conditions. The two specific random amplified polymorphic DNA (RAPD) fragments for the assay were identified on the basis of quantitative trait loci (QTL) analysis which were found to be tightly linked to cold sensitivity. The two RAPD fragments, OPT8(600) in the cold sensitivity rice cultivar 'Dular (indica)' and OPU20(1200) in the resistance rice cultivar 'Toyohatamochi (japonica)', were identified after screening 11 RAPD fragments using 2 random primers on the genomic DNAs of 'Dular' and 'Toyohatamochi'. These primers, when used in a multiplexed PCR, specifically amplified a 0.6 kb and a 1.2 kb fragment in the sensitive and resistant rice cultivars, respectively. When this assay was performed on the genomic DNAs of 16 japonica, 3 Tongil (indica/ japonica), and 2 indica rice cultivars, the primers amplified a 0.6 kb fragment in all of the cold sensitivity rice cultivars or 1.2 kb fragment in all of the resistance ones. These markers can be of potential use in the marker-assisted selection (MAS) for cold tolerance in rice seedling. As screening for resistance can now be conducted independent of the availability of low temperature, the breeding of cold tolerance cultivars can be hastened.     

Properties of phosphorylated myofibrils from gizzard smooth muscle

Phosphorylation of chicken gizzard myosin light chain in myofibril and its effect on myofibrillar ATPase activity were investigated in the contracted state of myofibrils. When myofibrils were incubated for two hours at 30 degreeds C with ATP, magnesium and calcium, the myosin light chain was phosphorylated by endogenous light-chain kinase. Standing overnight, the phosphorylated light chain was dephosphorylated by endogenous light-chain phosphatase. Control myofibril had much higher ATPase activity than phosphorylated and phosphorylated-dephosphorylated myofibrils. It was very interesting that the phosphorylated and phosphorylated-dephosphorylated myofibrils were quite similar in ATPase activity. However, phosphorylated myofibril differed from phosphorylated-dephosphorylated myofibril in Ca2+ dependency of Mg2+-ATPase activity. The phosphorylated-dephosphorylated myofibril was not affected by the presence or absence of Ca2+. In contrast, phosphorylated myofibril apparently showed a negative Ca2+-sensitivity. On the other hand, the results indicating that the superprecipitation gel formed by phosphorylated-dephosphorylated myosin could not be dissolved in 0.6 M NaCl, suggest that the phosphorylation-dephosphorylation process of the actomyosin system in gizzard myofibril results in stronger actin-myosin interaction.     

Study of thermodynamic properties of imidazolium-based ionic liquids and investigation of the alkyl chain length effect by molecular dynamics simulation

In this paper, structural and dynamical properties of five imidazolium-based ionic liquids (ILs) [amim]Br (a = methyl, ethyl, butyl, pentyl, hexyl) were studied by molecular dynamics simulations. United atom force field (UAFF) has been used for the representation of the interaction between ions. Good agreement with experimental data was obtained for the simulated density based on the UAFF. The calculated densities gradually decrease with an increase in the length of alkyl side chain, which is a result of weakening the electrostatic interaction between ions. The simulated heats of vaporisation are higher than that of non-ILs and decrease with an increase in temperature. Radial distribution function (RDF) was employed to analyse the local structure of ILs. Cation–anion RDFs show that the anions are well organised around the cation in two shells (0.41 and 0.6 nm). The velocity autocorrelation functions of the anion and cations show that the relaxation time increased with an increase in the length of the alkyl side chain. The diffusion coefficients of ions were calculated by mean square displacement of the centre of mass of the ions at 400 K. The calculated diffusion coefficients using UAFF agree well with other all atom force fields. Also diffusion coefficients decrease with an increase in the length of the alkyl side chain. The calculated transference numbers show that the cation contributes more than anion in the electrical current. The diffusion coefficients increase with temperature.     

Esterase 2-oligodeoxynucleotide conjugates as sensitive reporter for electrochemical detection of nucleic acid hybridization

A thermostable, single polypeptide chain enzyme, esterase 2 from Alicyclobacillus acidocaldarius, was covalently conjugated in a site specific manner with an oligodeoxynucleotide. The conjugate served as a reporter enzyme for electrochemical detection of DNA hybridization. Capture oligodeoxynucleotides were assembled on gold electrode via thiol-gold interaction. The esterase 2-oligodeoxynucleotide conjugates were brought to electrode surface by DNA hybridization. The p-aminophenol formed by esterase 2 catalyzed hydrolysis of p-aminophenylbutyrate was amperometrically determined. Esterase 2 reporters allows to detect approximately 1.5 x 10(-18)mol oligodeoxynucleotides/0.6 mm2 electrode, or 3 pM oligodeoxynucleotide in a volume of 0.5 microL. Chemically targeted, single site covalent attachment of esterase 2 to an oligodeoxynucleotide significantly increases the selectivity of the mismatch detection as compared to widely used, rather unspecific, streptavidin/biotin conjugated proteins. Artificial single nucleotide mismatches in a 510-nucleotide ssDNA could be reliably determined using esterase 2-oligodeoxynucleotide conjugates as a reporter.     

Detection and identification of a serine to arginine sequence variant in a therapeutic monoclonal antibody

Sequence variants, also known as unintended amino acid substitutions in the protein primary structure, are one of the critical quality attributes needed to be monitored during process development of monoclonal antibodies (mAbs). Here we report on analytical methods for detection and identification of a sequence variant in an IgG1 mAb expressed in Chinese hamster ovary (CHO) cells. The presence of the sequence variant was detected by an imaged capillary isoelectric focusing (ICIEF) assay, showing a new basic species in mAb charge variant profile. The new basic variant was fractionated and enriched by ion-exchange chromatography, analyzed by reduced light and heavy chain mass determination, and characterized by HPLC-UV/MS/MS of tryptic and endoproteinase Lys-C peptide maps. A Serine to Arginine sequence variant was identified at the heavy chain 441 position (S441R), and confirmed by using synthetic peptides. The relative level of the S441R variant was estimated to be in the range of 0.3-0.6% for several mAb batches analyzed via extracted ion chromatogram (EIC). This work demonstrates the effectiveness of using integrated analytical methods to detect and identify protein heterogeneity and the importance of monitoring product quality during mAb bioprocess development.     

Tryptic digestion of dynein 1 in low salt medium. Origin and properties of fragment A

Dynein 1 was extracted from sperm flagella of the sea urchin Tripneustes gratilla with 0.6 M NaCl and dialyzed against 0.5 mM EDTA, 14 mM 2-mercaptoethanol, 5 mM imidazole/HCl buffer, pH 7.0, for 24-48 h. In some cases, fractions containing the alpha heavy chain and the beta/intermediate chain 1 complex (beta/IC1) were separated by density gradient centrifugation in the same solution. Treatment of the samples at a trypsin:protein ratio of 1:10 w/w for 32 min at room temperature yields a crude digest from which Fragment A is purified by density gradient centrifugation. The purified Fragment A consists of two principal peptides (Mr = 195,000 and 130,000) that cosediment with the peak of ATPase activity at 12.5 S, which is slightly faster than the 11 S of the original beta/IC1 complex. When digests of the separated alpha chain and of the beta/IC1 complex are followed as a function of time, the early cleavages of the two heavy chains (Mr = 428,000) resemble each other in that both lead to similarly sized peptides of Mr 316,000 and 296,000, but only in the beta/IC1 fraction does the digestion proceed to form Fragment A. The remainder of the beta chain, termed Fragment B, occurs as an Mr 110,000 peptide sedimenting at 5.7 S with no associated ATPase activity. Fragment A has a specific ATPase activity of 4.3 mumol Pi X min-1 X mg-1, with a Km of 29 microM in 0.1 M NaCl medium, and an apparent Ki for inhibition by vanadate of 1.2 microM in the absence of salt, and 22 microM in 0.6 M NaCl. Photoaffinity labeling with [alpha-32P]8-azidoadenosine 5'-triphosphate indicates that the ATP binding site on the beta chain of dynein 1 is located on the Mr 195,000 peptide of Fragment A. The possibility that Fragments A and B of the beta/IC1 complex may correspond to the head and tail regions of the tadpole-shaped particle seen by electron microscopy is discussed.