Solution to a gene divergence problem under arbitrary stable nucleotide transition probabilities

Summary A nucleic acid chain L nucleotides in length, with the specific base sequence B₁B₂.B_L, each B_i being A, G, C, or T, is defined by the L-dimensional vector B = (B₁, B₂, , B_L), the k^th position in the chain being occupied by the base B_k. Let P_BB' be the twelve given constant non-negative transition probabilities that in a specified position the base B is replaced by the base B in a single step, and let P _BB' ^(XX) be the probability that the position goes from base B to B in X steps. An exact analytical expression for P _BB' ^(XX) is derived. Assuming that each base mutates independently of the others, an exact expression is derived for the probability P _BB' ^(XX) that the initial gene sequence B goes to a sequence B = (B₁, B₂, , B_L) after X = (X₁, X₂, , X_L) base replacements, where X_k is the number of single-step base replacements in the k^th position. The resulting equations allow a more precise accounting for the effects of Darwinian natural selection in molecular evolution than does the idealized but biologically less accurate assumption that each of the four nucleotides is equally likely to mutate to and be fixed as one of the other three. Illustrative applications of the theory to some problems in biological evolution are given.     

Sodium-transport NADH-quinone reductase of a marineVibrio alginolyticus

The respiratory chain of a marine bacterium,Vibrio alginolyticus, required Na⁺ for maximum activity, and the site of Na⁺-dependent activation was localized on the NADH-quinone reductase segment. The Na⁺-dependent NADH-quinone reductase extruded Na⁺ as a direct result of redox reaction. It was composed of three subunits, , , and , with apparentMr of 52, 46, and 32 KDa, respectively. The reduction of ubiquinone-1 to ubiquinol proceeded via ubisemiquinone radicals. The former reaction was catalyzed by the FAD-containing subunit. This reaction showed no specific requirement for Na⁺. For the formation of ubiquinol, the presence of the subunit and the FMN-containing subunit was essential. The latter reaction specifically required Na⁺ for activity and was strongly inhibited by 2-n-heptyl-4-hydroxyquinolineN-oxide. It was assigned to the coupling site for Na⁺ transport. The mode of energy coupling of redox-driven Na⁺ pump was compared with those of decarboxylase- and ATP-driven Na⁺ pumps found in other bacteria.     

N,N′-bis-(2,3-Methylenedioxyphenyl)urea and N,N′-bis-(3,4-methylenedioxyphenyl)urea enhance adventitious rooting in Pinus radiata and affect expression of genes induced during adventitious rooting in the presence of exogenous auxin

We have analyzed the effect of N,N′-bis-(2,3-methylenedioxyphenyl)urea (2,3-MDPU) and N,N′-bis-(3,4-methylenedioxyphenyl)urea (3,4-MDPU), two symmetrically substituted diphenylurea derivatives with no auxin or cytokinin-like activity, on the rooting capacity of Pinus radiata stem cuttings. Results indicate that both diphenylurea derivatives enhance adventitious rooting in the presence of exogenous auxin (indole-3-butyric acid, IBA), even at low auxin concentration, in rooting-competent cuttings, but have no effect on the adventitious rooting of low or null competent-to-root cuttings. Histological analyses show that, in the simultaneous presence of MDPUs and low concentration of exogenous auxin, adventitious root formation is induced in the cell types that retain intrinsic competence to form adventitious roots in response to auxin. The time course of cellular events leading to root formation and the time of root emergence are closely similar to that observed in cuttings treated only with higher auxin concentration. In addition, the mRNA level of a P. radiata SCARECROW-LIKE gene, which is significantly induced in the presence of the optimal concentration (10 μM) of exogenous auxin needed for cuttings to root, is increased in the presence of MDPUs and low concentration of exogenous auxin (1 μM). The expression of a P. radiata SHORT-ROOT gene in rooting-competent cuttings during adventitious rooting is also affected by the presence of MDPUs when combined with auxin. As MDPUs do not affect the expression of either gene in the absence of exogenous auxin, but only in its presence, we suggest that MDPUs could interact, directly or indirectly, with the auxin-signalling pathways in rooting-competent cuttings during adventitious rooting.     

Effect of various bud induction treatments on elongation and rooting of adventitious shoots of Canary Island pine (Pinus canariensis)

Three-day-old cotyledonary explants of Pinus canariensis were subjected to 30 induction treatments using half-strength Bornman's medium containing various combinations of N⁶- benzyladenine, zeatin, kinetin and 2-isopentenyl-adenine. The highest numbers of buds were obtained with 10 M 6-benzyladenine, but both kinetin and zeatin influenced shoot elongation. Shoots were maintained on half-strength Schenk and Hildebrandt medium with 2% sucrose and 0.05% activated charcoal. For rooting, shoots were pulsed for 4 h in a 100 M indole-3-butyric acid aqueous solution (pH 4.2–4.5), and planted in peat:vermiculite:perlite (1:1:1). After 8 weeks, the numbers of rooted shoots were similar for most treatments. Therefore, the bud induction treatments did not significantly influence rooting of adventitious shoots of Canary Island pine.     

Acclimation of barley to changes in light intensity: photosynthetic electron transport activity and components

Barley seedlings (Hordeum vulgare L. Boone) were grown at 20°C with 16 h/8 h light/dark cycle of either high (H) intensity (500 mole m^-2 s^-1) or low (L) intensity (55 mole m^-2 s^-1) white light. Plants were transferred from high to low (H L) and low to high (L H) light intensity at various times from 4 to 8 d after leaf emergence from the soil. Primary leaves were harvested at the beginning of the photoperiod. Thylakoid membranes were isolated from 3 cm apical segments and assayed for photosynthetic electron transport, Photosystem II (PS II) atrazine-binding sites (Q_B), cytochrome f(Cytf) and the P-700 reaction center of Photosystem I (PS I). Whole chain, PS I and PS II electron transport activities were higher in H than in L controls. Q_B and Cytf were elevated in H plants compared with L plants. The acclimation of H L plants to low light occurred slowly over a period of 7 days and resulted in decreased whole chain and PS II electron transport with variable effects on PS I activity. The decrease in electron transport of H L plants was associated with a decrease in both Q_B and Cytf. In L H plants, acclimation to high light occurred slowly over a period of 7 days with increased whole chain, PS I and PS II activities. The increase in L H electron transport was associated with increased levels of Q_B and Cytf. In contrast to the light intensity effects on Q_B levels, the P-700 content was similar in both control and transferred plants. Therefore, PS II/PS I ratios were dependent on light environment.Abbreviations Asc ascorbate - BQ 2,5-dimethyl-p-benzoquinone - DBMIB 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone - DCIP 2,6-dichlorophenolindophenol - H control plants grown under high light intensity - H L plants transferred from high to low light intensity - L low control plants grown under low light intensity - L H plants transferred from low to high light intensity - MV methyl viologen - P-700 photoreaction center of Photosystem I - Q_B atrazine binding site - TMPD N,N,N,N-tetramethyl-p-phenylenediamine Cooperative investigations of the United States Department of Agriculture, Agricultural Research Service, and the North Carolina Agricultural Research Service, Raleigh, NC. Paper No. 11990 of the Journal Series of the North Carolina Agricultural Research Service, Raleigh, NC 27695-7643, USA.     

The role of light and polar auxin transport in root regeneration from hypocotyls of tomato seedling cuttings

A relationship between light conditions, auxin transport and adventitious root formation by hypocotyls of tomato seedling cuttings was demonstrated. Effective rooting of tomato seedling cuttings was observed under continuous white light (WL) irradiation. However, root formation was reduced in darkness or under red (RL) or blue light (BL). At least 3/4-day-long irradiation treatment with (WL) was necessary to increase the number of roots formed in comparison with control cuttings grown in darkness. Light was most effective if applied during the first half of the 13-day-long rooting period. The role of photoreceptor-dependent light perception in the light-regulation of rooting was tested using tomato photomorphogenic mutants: aurea (au) and high pigment (hp). When exposed to WL both mutants generated fewer roots then their isogenic wild type (WT). In darkness or under BL and RL less roots were formed on all plants and no difference was observed between mutants and WT plants. TIBA (2,3,5-triiodobenzoic acid) inhibited rooting in a dose-dependent manner both in darkness and under WL. However, although rooting was suppressed by 0.75 M TIBA in the dark, 8 M TIBA was necessary to block root formation in continuous WL. Inhibition of rooting by TIBA was most efficient when applied at the initial period of rooting, a 1-day-long treatment with TIBA being sufficient to suppress rooting if given during the first 2 days of culture. Later treatment had much less effect on the root formation.     

Lysine Dendrimers and Their Starburst Polymer Derivatives: Possible Application for DNA Compaction and in vitro Delivery of Genetic Constructs

We attempted to find some compounds for the effective delivery of gene constructs into cells and obtained two trispherical dendrimers on the basis of lysine, (Lys)₈-(,-Lys)₄-(,-Lys)₂-(,-Lys)-Ala-NH₂ (D1) and ((Lys)₈-(,-Lys)₄-(,-Lys)₂-,-Lys)-Ala-[Lys(Plm)]₂-Ala-NH₂ (D2), as well as the starburst polymeric derivatives of D1, (pVIm) ₈ -D1 and (pLys) _n -D1, containing poly(N-vinylimidazole) and polylysine chains single-point bound to the dendrimer amino groups. The conditions of dendrimer–plasmid DNA complex formation were studied. The intracellular localization of these complexes and the expression of gene constructs delivered with their help were analyzed in transfection experiments on the HeLa cell cultures of human epithelial carcinoma and on mouse C2C12 myoblasts. It was found that the chemical structure of dendrimer D1 and its derivatives significantly affected the structure and properties of complex.     

Porosity and available water of temporarily waterlogged soils in a Quercus robur (L.) declining stand

Pedunculate oak (Quercus robur L.) is particularly sensitive to decline in clayey soils presenting a high-perched temporary water table. These soils induce two successive constraints in one-year cycle: water excess (and hypoxy) in winter and early spring, and water shortage in summer (water stress being more restrictive to oak). We determined the porosity and water properties of temporarily waterlogged clayey soils supporting forest stands of decliningQuercus robur trees in a 101yr-old oak stand in Belgium (50°06N, 4°16E). Roots unevenly colonized the soil down to 1.6m: fine roots (diameter<5mm) were mostly distributed on the surface horizons (0–0.3 m) and around 1.3m deep, despite dense clayey horizons appearing at 0.35m depth. Clay content below this depth reached 46–51. Illite and vermiculite were the dominant clay minerals. The clayey horizons exhibited marked shrink–swell properties: bulk density at 30kPa increased from 1.41 to 1.88gcm^–3 from the surface to 2m depth. There was also evidence of hypoxic conditions caused by water saturation of pore space in the rooting zone from October to mid-April. Extractable water (EW), calculated between moisture tensions of 5 and 1600kPa was 152.8mm. The level of perched temporary water table strongly depended on the seasonal rhythm of water uptake by trees and on the shrink–swell behaviour of soil.     

Heterogeneity of the α-globin gene defects in German α-thalassemia affected families

Summary Analysis of -thalassemia syndromes in several German families revealed DNA deletion as well as nondeletion forms as the molecular basis for the defects. Thus, the -thalassemia haplotype was identified as the (–)^3.7 rightward deletion form, and the region of the putative recombination process generating such a deletion was further characterized. In addition three different ° haplotypes, (--)^MED, (--)^>26, and ()^T, could be detected using -and -globin gene-specific probes.     

EEG-Driven Photic Stimulation Effect on Plasma Cortisol and β-Endorphin

The effect of EEG-driven photic stimulation on stress-related endocrine function was studied. Subjects were 16 healthy males divided into a photic stimulation group (n=8) and a control group (n=8). Electrodermal and emotional lability measures were assessed by nonspecific skin conductance response and the Maudsley Personality Inventory, respectively. Plasma cortisol and -endorphin concentrations were measured both before and after EEG-driven photic stimulation as well as the resting condition. Subjects with electrodermal, emotional, or both lability showed comparable decreases of plasma -endorphin on photic stimulation as did the stable subjects. Under resting control conditions, however, they showed significant increases of -endorphin compared to both stable subjects as well as the photic stimulation condition. In addition, labile subjects showed significant alpha enhancement on photic stimulation compared to stable subjects and to the resting control condition. The data suggest that increases of plasma -endorphin in labile control subjects may denote a stress response to the conditions of these experiments, and that any decrease by EEG-driven photic stimulation may indicate a reduction of responsiveness to an acute stress.     

Plant regeneration from hypocotyl segments of Lupinus luteus cv. L. Aurea

Complete plants of Lupinus luteus L. cv. Aurea that were regenerated from hypocotyl segments, bloomed, produced seeds and were efficiently nodulated by Bradyrhizobium sp. strains. The highest rates of shoot formation were obtained on A medium plus 1.3% agar with 10.0 M 2-isopentenyladenine (2iP) and 0.11 M naphthaleneacetic acid (NAA); the best rooting was achieved on a medium with 0.5 M NAA plus 0.05 M 2iP. Afterward, plantlets were transferred to either perlite or peat-containing pots and irrigated with a N-free nutrient solution until maturity. Direct rooting of hypocotyls could also be obtained on A medium with 1% agar.     

Synthesis of Cationic Amphiphiles on the Basis of Deoxycholic Acid

Cationic derivatives of deoxycholic acid with N,N-dimethylenediamine, -aminocaproic acid, and pyridine as polar heads were synthesized. The cationic groups were linked to 3- and 12-hydroxy groups of the steroid moiety through ester or urethane bonds. Liposomal formulations of the compounds synthesized may be used for gene delivery in cells.     

Zur Histochemie von Hydrolasen im Hoden des Hundes und der Katze

Zusammenfassung Wir untersuchten das Verteilungsmuster von unspezifischer Esterase, alkalischer Phosphatase, Adenosintriphosphatase, 5-Nucleotidase und -D-Glucuronidase im Hoden von Hund und Katze. Besonders hervorzuheben sind eine starke Aktivität der unspezifischen Esterase in den Sertolizellen der Katze, der Reichtum der Membrana propria aller Hodentubuli an alkalischer Phosphatase und Adenosintriphosphatase sowie die kräftige Reaktion auf -D-Glucuronidase in den Leydigzellen beider Tierarten.Die Befunde werden diskutiert.

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Summary The localization of unspecific esterase, alkaline phosphatase, adenosine triphosphatase, 5-nucleotidase, and -D-glucuronidase in the testes of cat and dog was demonstrated by histochemical means. We observed a strong esterase activity in the Sertoli cells of the cat and high amounts of alkaline phosphatase and adenosine triphosphatase in the membrana propria of all seminiferous tubules. In both species the principal site of -D-glucuronidase was in the Leydig cells. Our findings obtained being discussed.

     

Synthesis of nitrodiazirinyl derivatives of neurotoxin II fromNaja naja oxiana and their interaction with theTorpedo californica nicotinic acetylcholine receptor

Five singly modified nitrodiazirine derivatives of neurotoxin II (NT-II) fromNaja naja oxiana were obtained after NT-II reaction with N-hydroxysuccinimide ester of {2-nitro-4 [3-(trifluoromethyl)-3H-diazirin-3yl]phenoxy}acetic acid followed by Chromatographic separation of the products. To localize the label positions, each derivative was first UV-irradiated and then subjected to reduction, carboxymethylation, and trypsinolysis. Tryptic digests were separated by reversed phase-HPLC, the labeled peptides being identified by mass spectrometry. The derivatives containing the photolabel at the position Lys 25, Lys 26, Lys 44, or Lys 46 were [¹²⁵I]iodinated by the chloramine T procedure. Each iodinated derivative was found to form photoinduced cross-links with the membrane bound nicotinic acetylcholine receptor (AChR) fromTorpedo californica. The pattern of labeling the receptor's, , , or subunits was dependent on the photolabel position in the NT-II molecule and differed from that obtained earlier with an analogous series ofp-azidobenzoyl derivatives of NT-II. The results obtained indicate that (i) different sides of the neurotoxin molecule are involved in the AChR binding, and (ii) fragments of the different AChR subunits are located close together at the neurotoxin-binding sites.Abbreviations AChR Acetylcholine receptor - NDPA [2-nitro-4-[3-(trifluoromethyl)-3H-diazirin-3-yl]]phenoxy]acetyl - NT-II neurotoxin II     

Carbohydrate Structural Units in Glycosphingolipids as Receptors for Gal and GalNAc Reactive Lectins

Glycosphingolipids (GSLs) contain many carbohydrate epitopes or crypto-glycotopes for Gal and GalNAc reactive lectins. Many of them are in the nervous system and function as important receptors in various life processes. During the past two decades, 11 mammalian structural units have been used to express the binding domain of applied lectins. They are: F, GalNAc1 3GalNAc; A, GalNAc1 3Gal; T, Gal1 3GalNAc; I, Gal1 3GlcNAc; II, Gal1 4GlcNAc; B, Gal1 3Gal; E, Gal1 4Gal; L, Gal1 4Glc; P, GalNAc1 3Gal; S, GalNAc1 4Gal, and Tn, GalNAc1 Ser(Thr). Although 10 of them occur in GSLs, only 3 (L , S , and T ) are found in human brain, and 2 (L and II ) are present in the inner structures of human blood group active GSLs. In the families of gangliosides, L and II represent 55% of the total structural units, while the other three units (T , P , and S ) constitute the rest. To facilitate the selection of lectins that could serve as structural probes, the carbohydrate binding specificities of Gal/GalNAc reactive lectins have been classified according to their highest affinity for the structural units and their binding properties expressed by decreasing order of reactivity. Hence, the binding relation between GSLs and Gal/GalNAc specific lectins can be established.     

Regeneration of fertile plants from protoplasts of different Arabidopsis thaliana genotypes

Summary A protocol for obtaining regenerated fertile plants from mesophyll protoplasts of Arabidopsis thaliana is reported. Protoplasts were isolated from leaves of 21-to 28-day-old Arabidopsis plants grown in a controlled environment. Sustained divisions were achieved when protoplasts were embedded in beads formed by 1.4% sodium alginate in the presence of 50mM CaCl₂ in 0.4 mannitol, which was then exchanged againts modified B5 medium. About 0.4%–0.6% of the protoplasts developed into colonies of which 80%–90% formed shoots and subsequently regenerated to fertile plants. Seeds harvested from more than 200 independently regenerated plants were sown and germination frequencies of more than 95% were obtained. Furthermore, the F₁ plants did not show any evidence of somaclonal variation on visual inspection. This protocol was originally developed for Arabidopsis thaliana Columbia; however it was shown to be applicable also for the genotypes Wassilewskija, Landsberg erecta and Estland though with differing efficiencies.Abbreviations FDA fluorescein diacetate - CM culture medium - SRM shoot regeneration medium - SEM shoot elongation medium - RM rooting medium - PE plating effciency - NAA -naphthaleneacetic acid - 2,4-D 2,4-dichlorophenoxyacetic acid - IAA indole-3-acetic acid - IBA indole-3-butyric acid - BAP 6-benzylaminopurine - Kin kinetin - 2-iP 2-isopentenyladenine - GA₃ gibberetic acid     

Microbial transformation of ginsenoside Rb1 by Rhizopus stolonifer and Curvularia lunata

Of 49 microbial strains screened for their capabilities to transform ginsenoside Rb₁, Rhizopus stolonifer and Curvularia lunata produced four key metabolites: 3-O-[-d-glucopyranosyl-(1,2)--d-glucopyranosyl]- 20-O-[-d-glucopyranosyl]-3,12, 20(S)-trihydroxydammar-24-ene (1), 3-O-[-d-glucopyranosyl-(1,2)--d- glucopyranosyl]-20-O-[-d-glucopyranosyl]-3,12, 20(S)-trihydroxydammar-24-ol (2), 3-O-[-d-gluco- pyranosyl-(1,2)--d-glucopyranosyl]-3, 12, 20(S)-trihydroxydammar-24-ene (3), and 3-O--d-glucopyranosyl-3, 12, 20(S)-trihydroxydammar-24-ene (4), identified by TOF-MS, ¹H- and ¹³C-NMR spectral data. Metabolites 1, 3 and 4 were from the incubation with R. stolonifer, and 1 and 2 from the incubation with C. lunata. Compound 2 was identified as a new compound.     

Plantlet multiplication from white pine (Pinus strobus L.) embryos in vitro: bud induction and rooting

White pine embryos were grown on 4 different media with 6 different benzyladenine (BA) concentrations. Maximum adventitious shoot initiation and growth were obtained on a modified Lepoivre medium with 20 M BA. Modified Schenk and Hildebrandt, Murashige and Skoog, and Gresshoff and Doy media were also tested. Shoot elongation was achieved on half-strength basal medium lacking growth regulators. Three rooting experiments involving indole-3-butyric acid (IBA), sucrose concentration, shoot orientation, IBA pulse length, and light or dark were carried out. Treatment of shoots in an upright position with 50 M IBA for eight days followed by culture in a medium with 3% sucrose in the light produced the most rooting (50% at 3 months). Rooted shoots were transplanted to the greenhouse for further growth.     

Taxonomical significance of the leaf indument inDryopteris (Pteridophyta): I. Some North American,Macaronesian and European taxa

The leaf indument of a number of North American, Macaronesian and EuropeanDryopteris taxa is described. Trichome characters provide very useful taxonomical data for the study of species complexes and for tracing relationships among geographically isolated or separated taxa. The new combination,D. expansa var.alpina, is made. The present study sustains best theWagner D. semicristata relationship scheme.     

Membrane adenosine triphosphatase of Micrococcus lysodeikticus. Isolation of two forms of the enzyme complex and correlation between enzymatic stability,latency and activity.

Summary Two new forms of the plasma membrane ATP-ase ofMicrococcus lysodeikticus NCTC 2665 were isolated from a sub-strain of the microorganism by polyacrylamide gel electrophoresis. One of them had a mol.wt of 368,000 and a very low specific activity (0.80 µ mol.min^–1.mg protein^–1) that could not be stimulated by trypsin. This form has been called B^I (strain B, inactive). If the electrophoresis was carried out in the presence of reducing agents (i.e., dithiothreitol) and the pH of the effluent maintained at a value of 8.5 another form of the enzyme was obtained. This had a mol.wt of 385,000 and a specific activity of 2.5–5.0 µ mol.min^–1.mg protein^–1 that could be stimulated by trypsin to 5–10 µ mol.min^–1.mg protein^–1. This preparation of the ATPase has been called form B_A (strain B, enzyme active). The subunit composition of both forms has been studied by sodium dodecyl sulphate and urea gel electrophoresis and compared to that of the enzyme previously purified from the original strain (form A). The three forms of the enzyme had similar and subunits, with mol.wt of about 50,000 and 30,000 dalton, respectively. They also had in common the component(s) of relative mobility 1.0, whose status as true subunit(s) of the enzyme remains yet to be established. However, subunit, that had a mol.wt of about a 52,500 in form A (Andreu et al. Eur. J. Biochem. (1973) 37, 505–515), had a mol.wt similar to in form B_I and about 60,000 in form B_A. Furthermore B_A usually showed two types of this subunit ( and) and an additional peptide chain () with a mol.wt of about 25,000 dalton. This latter subunit seemed to account for the stimulation by trypsin of form B_A.Forms B_A could be converted to B_I by storage and freezing and thawing. Conventional protease activity could not be detected in any of the purified ATPase forms and addition of protease inhibitors to form B_A failed to prevent its conversion to form B_I. The low activity form (B_I) was more stable than the active forms of the enzyme and also differed in its circular dichroism. These results show thatM. lysodeikticus ATPase can be isolated in several forms. Although these variations may be artifacts caused by the purification procedures, they provide model systems for understanding the structural and functional relationships of the enzyme and for drawing some speculations about its functionin vivo.