Determination of the backbone torsion angle ɛ in nucleic acids

Summary The multiplet structure of cross peaks in double-quantum-filtered COSY NMR spectra is analysed for those resonances that include passive heteronuclear couplings. Interestingly, the cross peak involving the sugar-ring protons H2 and H3 in nucleic acids display an E.COSY-type appearance exclusively when the backbone torsion angle (C4-C3-O3-P) adopts a gauche(-) conformation. This observation allows an unambiguous analysis of the conformation around , without the knowledge of ³J_cp coupling constants.     

Dose-dependent nonlinear response of the main phase-transition temperature of phospholipid membranes to alcohols

Summary The effect of 1-alkanols upon the main phase-transition temperature of phospholipid vesicle membranes between gel and liquid-crystalline phases was not a simple monotonic function of alkanol concentration. For instance, 1-decanol decreased the transition temperature at low concentrations, but increased it at high concentrations, displaying a minimal temperature. This concentration-induced biphasic effect cannot be explained by the van't Hoff model on the effect of impurities upon the freezing point. To explain this nonlinear response, a theory is presented which treats the effect of 1-alkanols (or any additives) on the transition temperature of phospholipid membranes in a three-component mixture. By fitting the experimental data to the theory, the enthalpy of the phase transition H ^* and the interaction energy, _AB ^* between the additive and phospholipid molecules may be estimated. The theory predicts that when _AB ^* >2 (where _AB ^* = _AB,/RT _o,T _o being the transition temperature of phospholipid), both maximum and maximum transition temperatures should exist. When _AB ^* = 2, only one inflection point exists. When _AB ^* < 2, neither maximum nor minimum exists. The alkanol concentration at which the transition temperature is minimum (X _min) depends on the _AB ^* value: the larger the _AB ^* values, the smaller theX _min. When _AB ^* is large enough,X _min values become so small that the plot T vs.X shows positive T in almost all alkanol concentrations. The interaction energy between 1-alkanols and phospholipid molecules increased with the increase in the carbon chain-length of 1-alkanols. In the case of the dipalmitcylphosphatidylcholine vesicle membrane, the carbon chain-length of 1-alkanols that caused predominantly positive T was about 12.     

Plant chaperonins: a role in microtubule-dependent wall formation?

Summary The cytosolic chaperonin containing t-complex peptide-1 (CCT) is involved in the correct folding of newly synthetized actin and tubulin molecules. To get insight into potential additional functions of plant CCT, the localization of the subunit CCT was followed throughout cell cycle, cell elongation, and cell differentiation in the tobacco cell culture VBI-O with relation to the microtubular cytoskeleton by double-immunofluorescence and confocal microscopy. The CCT subunit was found to colocalize with sites of microtubule nucleation such as nuclear envelope and preprophase band. In addition, CCT was associated with tubulin in sites of elevated wall synthesis such as phragmoplast or along secondary-wall thickenings. CCT and its substrate tubulin were found to be soluble during periods of cytoskeletal dynamics, whereas sedimentable, vesicle-bound forms of CCT and tubulin prevailed during cell differentiation. The sedimentability of CCT was increased by calcium, whereas it was detached from microsomes by ATP. CCT can bind to both polymerized microtubules and tubulin dimers. These data suggest an additional function of plant CCT in microtubule-driven transport of vesicles that contain cell-wall material.Abbreviations CCT cytosolic chaperonin containing t-complex polypeptide 1     

On the phytochrome phototransformation kinetics in mustard seedlings

Summary The in vivo phototransformation kinetics of mustard hook and cotyledon phytochrome exhibit a deviation from a single first order curve, quite similar to that for pumpkin hooks as reported in a previous paper (Boisard, Marmé and Schäfer, 1971). The P _frP_rkinetics can be characterized by the ratios _fr, ^I · P _fr ^I / _fr, ^II · P _fr, ^II and where P _fr ^I and P _fr ^II are two populations of phytochrome molecules which convert to P _rwith a first order half-life of and . These ratios depend on the length of time of etiolation. The ratio _fr, ^I · P _fr ^I / _fr, ^II · P _fr, ^II is independent of the amount of total P _frpresent at the beginning of the P _frP_rphototransformation after a non-saturating dose of red light. The half-lives of the two populations, however, depend on the concentration of total P _frinitially present. P _frP_rphototransformation kinetics with different light intensities show that reciprocity holds.     

Potential induced in a spherical cell by an intracellular point source and an extracellular point sink

Summary The potential is calculated for all time, inside and outside a spherical cell for a point source of current inside the cell and a point sink located a finite distance outside the cell. The source and sink are step functions in time. An eigenfunction expansion is obtained, valid for arbitrary =_m a/_i , where _i and _m are the conductivities inside the cell and in the membrane, respectively, a is the cell radius and the membrane thickness. For small , the eigenfunction expansion is expanded in powers of . The time dependence of the potential contains transients with two widely differing time constants =C_m a/_i, where C_m is the membrane surface capacitance, and _m=/. Closed-form expressions are obtained for the two leading terms, for small , after the rapid transient is over. The remaining time dependence is only in the potential inside the cell, and is a simple exponential increase, independent of position within the cell. It is found that the transmembrane potential is insensitive to the location of the extracellular sink at long times, but not at short times. The dependence of the potential on location of source, sink, and observer is studied for long times after the quick transients are over. A uniqueness theorem is derived for the solution to Laplace's equation for the membrane boundary condition.This work was supported in part by NSF Grant No. GB-24965. Dr. Peskoff is the recipient of NIH Special Research Fellowship No. 1F03 GM 55849-01. Mr. Ramirez is a Ford Foundation Pre-doctoral Fellow.     

Saccharomyces cerevisiae DNA repair processes: an update

The effect of incubating T3-1 cells with phorbol 12,13-dibutyrate (PDBu) on the protein kinase C (PKC) isoform content (predominantly , and isoforms) was assessed by immunoblotting, enzyme activity assay and [³H]PDBu binding. After exposure to PDBu for 17 h the immunoreactivity detected for both PKC and PKC had disappeared from cytosol and had increased slightly in membranes. Immunoreactivity for PKC was present as two bands in cytosol; after PDBu treatment both bands decreased in intensity, the higher molecular weight band more than the lower. The lower molecular weight band corresponded with a component of constitutive PKC activity eluting from DEAE cellulose that was defined by inhibition of basal activity with GF 109203X or H7. Investigation of very short treatment times with PDBu using binding, immunoblot and activity measurements (in the presence/absence of Ca²⁺) indicated that translocation of PKC and was very rapid — detectable by 10 sec, maximal within minutes. Reduction of these isoforms in membranes took much longer, and was not apparent up to 150 min. The immunoblot data for PKC in cytosol showed no detectable effect of PDBu treatment on the low molecular weight band up to 150 min although it was reduced at 17 h. Translocation of the upper band was detectable at 10 sec but this band may have resulted from cross-reaction with other PKC isoforms. The constitutive activity and low molecular weight (authentic) PKC immunoreactivity were partially affected after long exposure only, suggesting an action of PDBu on PKC secondary to activation of the other PKC isoforms. An endogenous receptor agonist, luteinising hormone-releasing hormone (LHRH), was also used to assess by immunoblotting, translocation of the PKC isoforms. Although all the isoforms did translocate from cytosol to membrane fractions, they did so with distinctly different time courses: PKC moved more rapidly than PKC which appeared to translocate more quickly than PKC . After downregulation of the responsive PKC isoforms with PDBu, the remaining PKC was not translocated by LHRH. (Mol Cell Biochem 165: 65–75, 1996)     

Comparison of three granular support materials for anaerobic fluidized bed systems

Summary Three different materials, kaolin, pozzolana and biolite (a material used in a commercial anaerobic fluidized bed treatment process) when tested as supports for an anaerobic fluidized bed system had similar physical and fluidization properties but behaved differently towards the biomass hold-up. However, all three systems attained similar removal efficiency rates.Nomenclature U Fluidization velocity (m/s) - U₁ Terminal fluidization velocity (m/s) - g Local acceleration due to gravity (m/s²) - _s Solid density (kg/m³) - _f Fluid density (kg/m³) - P Pressure drop (Pa) - HRT Hydraulic retention time (days) - H_mf Height of bed at minimum fluidization (m) - H Height of bed (m) - C_d Drag coefficient (dimensionless) - W Mass of solids in bed (kg) - dp Particle diameter (m) - A Cross-sectional area of column (m²) - h column height (m) - Rc_t Terminal Reynolds no. - Voidagc (fractional free volume, dimensionless) - _mf Voidage (fractional free volume) at minimum of fluidization (dimensionless)     

Characterization and expression analysis of CD3ɛ and CD3γ/δ in fugu, Takifugu rubripes

CD3 is an essential component of the CD3-TCR complex. In this report, we describe the cloning, characterization, and expression analysis of the CD3 and CD3/ chain genes from fugu, Takifugu rubripes. Two distinct CD3 homologue cDNAs, designated as CD3-1 and CD3-2, and a CD3/ homologue cDNA were isolated from the fugu thymus. The deduced amino acid sequences of these cDNAs exhibit conserved essential CD3 chain motifs and overall structures. RT-PCR analysis demonstrated that the CD3 and CD3/ genes were expressed in lymphoid organs (e.g. thymus, head kidney, trunk kidney and spleen), mucosal tissues (gill, skin, and intestine), and peripheral blood leucocytes (PBL). The CD3 and TCR genes were expressed only in the surface IgM^– population, which were separated from PBL using an anti-fugu IgM monoclonal antibody. In addition, in situ hybridization confirmed that CD3-expressing cells were distributed randomly in the head kidney, trunk kidney, and spleen, but in the thymus were restricted to the lymphoid outer zone and epithelioid inner zone only. Collectively, these results suggest that CD3 molecules are useful markers for the identification of T cells in teleost fish. The present study thus provides a critical step in identifying T cells in this model organism.Nucleotide sequence data reported in this paper are available in the DBJ/EMBL/GenBank databases and have been assigned the accession numbers AB166798 (CD3-1), AB166799 (CD3-2), and AB166800 (CD3/).     

Estimation of entropy of a binary variable: Satisfying a reliability criterion

Entropy of a binary variable X can be estimated from frequencies calculated on the basis of N observations. The paper considers a reliability criterion of the form Prob(¦H–H_N¦<)1– where H and H _N are the true and estimated entropies respectively, and and define the reliability criterion. A procedure is suggested in which N is incremented until the probability is at least 1– but less than 1–/2, satisfying the criterion but avoiding a needlessly extravagent number of observations.     

Sugar conformation of a stereospecific 2′-R or 2′-S deuterium-labeled DNA decamer studied with proton-proton J coupling constants

The sugar conformation of a DNA decamer was studied with proton-proton ³J coupling constants. Two samples, one comprising stereospecifically labeled 2-R-²H for all residues and the other 2-S-²H, were prepared by the method of Kawashima et al. [J. Org. Chem. (1995) 60, 6980–6986; Nucleosides Nucleotides (1995) 14, 333–336], the deuterium labeling being highly stereospecific 99% for all 2-²H, 98% for 2-²H of A, C, and T, and 93% for 2-²H of G). The ³J values of all H1-H2 and H1-H2 pairs, and several H2-H3 and H2-H3 pairs were determined by line fitting of 1D spectra with 0.1–0.2 Hz precision. The observed J coupling constants were explained by the rigid sugar conformation model, and the sugar conformations were found to be between C3-exo and C2-endo with _m values of 26° to 44°, except for the second and 3 terminal residues C2 and C10. For the C2 and C10 residues, the lower fraction of S-type conformation was estimated from J_H1H2 and J_H1H2 values. For C10, the N–S two-site jump model or Gaussian distribution of the torsion angle model could explain the observed J values, and 68% S-type conformation or C1-exo conformation with 27° distribution was obtained, respectively. The differences between these two motional models are discussed based on a simple simulation of J-coupling constants.     

Effective diffusivity and tortuosity in a porous glass immobilization matrix

The effective diffusivity of glucose in porous glass beads was determined using a transient method. Predictions for the intraparticle and surface concentrations were made by an analytical solution of the mass balance. The value of the diffusivity was expected to be lower than the value of the corresponding diffusion coefficient in water, but the opposite was observed. This effect results from intraparticle fluid flow, leading to high values of the apparent effective glucose diffusivity. To measure diffusion only and to prevent any internal convection during the diffusion experiment, the pores of the porous glass beads were filled with Ca-alginate gel. For these glass beads (internal porosity, , equal to 0.56), we found an effective glucose diffusivity of 2.2×10^–10 m²/s at 30°C. Using the relationship to effective intraparticle diffusivity (D_eff)=effective diffusivity in 1% Ca-alginate beads (D_gel) / (with the tortuosity factor) this gives =1.7. For known and measuring by the method described, the D_eff can be calculated for other porous materials or diffusing substances. Knowledge of the exact value of the effective diffusivity is a necessity in bioreactor modelling and was demonstrated by prediction of the residence time distribution profiles in a packed-bed bioreactor containing immobilized yeast cells.     

Identification of post-translational modified amino acids

Summary Methylated lysines (N -mono-methylated, N -di-methylated and N -tri-methylated) have been identified after derivatization with orthophthaldialdehyde (OPA) by using pre-column and post-column derivatization techniques.Also the N -acetylated lysine and N -formylated lysine have been identified by OPA post-column derivatization techniques but only in free form due to their instability under acidic conditions which are used for protein hydrolysis.Additionally, all the modified amino acids mentioned above have been derivatized with DABITC/PITC, an Edman reagent, and identified as DABTH-derivatives on thin-layer polyamide sheets.     

Effects of midazolam on the contraction and relaxation of segments of thoracic aorta stripped of endothelium and stimulated by adrenaline – experimental study in rabbits

To evaluate the effects of midazolam on the angiokinesis of segments of rabbits' thoracic aorta stripped of endothelium and stimulated by adrenaline.Two groups of aortic rings removed from albinic rabbits anesthetized with thiopental were used (Group I – 6 animals; Group II – 12 animals), stripped of endothelium, studied in an organ chamber, perfused by Krebs-Henseleit solution. The groups were stimulated by adrenaline, recording the maximum contraction and dT/dt at 12, 36, 60 and 120. When the plateau phase was reached, the vessel was washed with perfusion solution, recording relaxation at 2, 4 and 6. When the base values were reached, Group I underwent a new adrenergic stimulus; and Group II was stimulated with midazolam and then with adrenaline, and the same values were recorded. T test was applied as a statistical analysis when two variables were studied. When studying more than two variables the Anova test was used, supplemented by the Tuckey test.Group I did not show any significant difference between the two stimuli. Group II – the midazolam significantly reduced the maximum contraction induced by adrenaline (83.01 ± 4.11%) (p < 0.01). The dT/dt was reduced at 12 (57.06 ± 8.47%), and also at 36 (70.59 ± 5.26%). There was no significance at 60 and 120 (p < 0.01).The relaxation increased significantly at all measurements – at 2-adrenaline 39.31 ± 9.60%; adrenaline/midazolam: 44.06 ± 9.62% (p < 0.05). At 4-adrenaline: 53.08 ± 8.3%; adrenaline/midazolam: 61.68 ± 8.50% (p < 0.01). At 6-adrenaline: 76.26 ± 5.45%; adrenaline/midazolam: 84.20 ± 7.96% (p < 0.01).Midazolam significantly reduced the maximum contraction obtained by the adrenergic stimulus as well as the dT/dt in the initial phases of contraction. The relaxation speed also increased.     

Synthesis of N<Subscript>ɛ</Subscript>-protected-L-lysine and γ-benzyl-L-glutamate N-carboxyanhydrides (NCA) by carbamoylation and nitrosation

Summary. This paper reports on an original process to synthesize N-carboxyanhydrides, which consists of nitrosating N-carbamoylamino acids with a NO/O₂ gas mixture in acetonitrile. The synthesis of several N-carbamoylamino acids of L-lysine was described using potassium cyanate in water. The latter were then nitrosated to yield the corresponding NCA with more or less efficiency. Indeed, the NCA carrying an acid-sensitive protecting group led to a partial deprotection to give the L-lysine NCA salt. The NCA of N-trifluoroacetyl-L-lysine, N-benzyloxycarbonyl-L-lysine and -benzyl-L-glutamate were successfully synthesized with satisfactory yields. Their polymerizability was compared to that of the N-trifluoroacetyl-L-lysine NCA initiated by n-hexylamine in N,N-dimethylformamide. It also showed that this new process of NCA synthesis could be applied to the synthesis of polypeptides and more generally to the protein chemistry.     

Heteropolynucleotides as templates for non-enzymatic polymerizations

Summary We have studied a number of condensation reactions involving ImpU, ImpT, ImpC, ImpA, ImpG, ImpUpG and ImpCpA as activated nucleotide donors and a variety of homo- and hetero-polynucleotides as templates. We did not obtain any evidence of a template effect with ImpU and ImpT, but observed some condensation of ImpC with GpG on appropriate templates. ImpA and ImpG take part in a number of more or less efficient template-directed reactions, as do ImpUpG and ImpCpA.Our results suggest that, on the primitive Earth, pyrimidine nucleotides could most easily have been incorporated into polymers as constituents of short oligomers, which contained one or more purine nucleotide. The linkage of the product depends strongly on the nature of the substrates; the percentage of the natural 3-5-linkage was, in some cases, less than 10% and, in others, as high as 70%. Wobble-pairing was often very effective in promoting condensations, suggesting that transition mutations would have been very frequent in prebiotic polynucleotide replication.Abbreviations and Conventions U uridine - T thymidine - C cytidine - A adenosine - G guanosine - pN nucleoside-5-phosphate - Np a mixture of 2- and 3-phosphates of a nucleoside - pNp a mixture of the 2-5-diphosphate and 3-5-diphosphate of a nucleoside - N₁ ² pN₂ a 2-5-linked dinucleoside monophosphate - N₁ ³ pN₂ a 3-5-linked dinucleoside monophosphate - N⁵ ppN a pyrophosphate derived from a nucleoside-5-phosphate. ImpN and ImpN₁pN₂ are 5-phosphorimidazolides of nucleosides and 3-5-linked dinucleoside monophosphates, respectively - poly(N) a homopolynucleotide - poly (U₁ C₂ A₄ G₃) a random copolymer derived from a substrate mixture containing U, C, A, G in ratio 1:2:4:3 - ODU optical density units measured at 260 nm     

Structural analyses of new tri- and tetrasaccharides produced from disaccharides by transglycosylation of purified Trichoderma viride β-glucosidase

A new -glucosidase was partially purified from Trichoderma viride cellulase. This -glucosidase catalyzed a transglycosylation reaction of cellobiose to give -D-Glc-(16)--D-Glc-(14)-D-Glc (1, yield: 18.8%) and -D-Glc-(16)--D-Glc-(16)--D-Glc-(14)-D-Glc (2, 3.7%), regioselectively. Furthermore, the enzyme regioselectively converted laminaribiose and gentiobiose into -D-Glc-(16)--D-Glc-(13)-D-Glc (3, 15.3%) and -D-Glc-(16)--D-Glc-(16)-D-Glc (4, 20.2%), respectively. The structures (1–4) of the products were determined by ¹H and ¹³C NMR spectroscopies. This high regio- and stereoselectively of the -glucosidase could be applied for oligosaccharide synthesis.     

Association of RFLP markers with loci conferring broad-based resistance to the soybean cyst nematode (Heterodera glycines)

Soybean cyst nematode (SCN) is a major soybean yield-limiting pest. The present study was conducted to map broad-based SCN resistance loci from the cultivar Hartwig. Two-hundred F₂₃ lines derived from the cross Williams 82 x Hartwig were screened with a fourth-generation SCN inbred and 56 polymorphic molecular markers. Allele states and phenotypes were analyzed using stepwise regression and the model selection was made at P 0.01. Four unlinked RFLP markers (A006, A567, A487, A112) were associated with SCN resistance and the partial coefficient of determinations (R²) were 91%, 1%, 1%, and 1%. We have mapped a new, major SCN resistance locus (A006) and three minor loci (A567, A487, A112). This complete mapping will accelerate the transfer of broad-based resistance without linkage drag and aid in the determination of relationships among various SCN-resistant germplasm sources.     

A case of hereditary persistence of fetal hemoglobin caused by a gene not linked to the β-globin cluster

Summary The pattern of inheritance of several polymorphic restriction sites associated with the -gene cluster, and spanning a region of 52 kb, demonstrates that a determinant for hereditary persistence of fetal hemoglobin (HPFH) segregates independently from the non- globin gene cluster, as we postulated several years ago on purely genetical grounds. This finding provides additional evidence for the existence of diffusible factors affecting -chain expression. Moreover, we have identified a private HinccII polymorphism, in the vicinity of the gene in the family studied.     

Comparative study on the chloroplast,mitochondrial and nuclear genome differentiation in two cultivated rice species,Oryza sativa and O. glaberrima,by RFLP analyses

Summary Restriction fragment length polymorphisms of chloroplast (ct), mitochondrial (mt) and nuclear DNA were investigated using eight cultivars of Oryza sativa and two cultivars of O. glaberrima. Relative variability in the nuclear and cytoplasmic genomes was estimated by a common measure, genetic distance. Based on the average genetic distances among ten cultivars for each genome, the evolutionary variabilities of the mitochondrial and nuclear genomes were found to be almost the same, whereas the variability of the chloroplast genome was less than half that of the other two genomes. Cluster analyses on ct and mt DNA variations revealed that chloroplast and mitochondrial genomes were conservative within a taxon and that their differentiations were well-paralleled with respect to each other. For nuclear DNA variation, an array of different degrees of differentiation was observed in O. sativa, in contrast with little variation in O. glaberrima. As a whole, differentiation between O. sativa and O. glaberrima was clearly observed in all three genomes. In O. sativa, no notable difference was found between the cultivars Japonica and Javanica, whereas a large differentiation was noticed between Japonica (including Javanica) and Indica. In all three genomes, the average genetic distances within Indica were much larger than those within Japonica (including Javanica), and almost similar between Japonica (including Javanica) and Indica. These facts indicate that differentiation in O. sativa was due mainly to Indica.     

Stereospecificity and electrogenicity of amino acid transport in Riccia fluitans

In the aquatic liverwort Riccia fluitans, membrane depolarization (_m), change in membrane conductance (g_m), and current-voltage (I-V) characteristics in the presence of different amino acids as well as the uptake of ¹⁴C-labeled amino acids were measured. L-isomers of the tested amino acids generate larger electrical effects (_m, g_m) than D-isomers, and the I-V characteristics show that the positive electrical inward-current of 20 mA m^-2 generated by 0.5 mM D-serine is only about 50% of the current generated by adding 0.5 mM L-serine. Whereas - and -amino acids rapidly depolarize the membrane to the same extend, with -aminobutyric acid (-AB) and dipeptides no significant electrical effects have been measured. The uptake kinetics of ¹⁴C-labeled amino acids display three components: (I) A saturable high-affinity component with K_s-values of 48 M D-alanine, 12 M -aminoisobutyric acid (AIB), 9 M L-alanine, 8 M L-proline, and 6 M L-serine, respectively; (2) an apparently linear low-affinity component, and (3) an also linear but unspecific component at concentrations >20 times the given K_s-value. Uptake of ¹⁴C-labeled AIB can be inhibited competitively by all tested neutral amino acids, the L-isomers being more effective than the D-isomers, as well as by ammonium or methylamine. Vice versa, AIB competitively inhibits uptake of L-serine and L-alanine. It is concluded that an uncharged stereospecific carrier for the investigated amino acids exists in the plasmalemma of Riccia fluitans. Accumulation ratios of about 50 suggest secondary active transport driven by a transmembrane electro-chemical gradient (mainly _m) which is generated by the electrogenic proton pump. It is suggested that this carrier binds to the amino group forming either a charged binary complex with positively charged amines (Felle 1980), or an uncharged complex with -AB or dipeptides, whereas electrogenic transport of - and -amino acids is mediated by a ternary carrier complex, probably charged by a proton.Symbols and Abbreviations _m membrane potential (mV) - E_co equilibrium potential (mV) of the transport system - g_m membrane (slope) conductance (Sm^-2) - g_m change in g_m - I-V curve current-voltage curve - AIB -aminoisobutytric acid - -AB -aminobutyric acid