DNA Isolation and AFLP™ Genetic Fingerprinting of shape Theobroma cacao (L.)

Accurate identification of parental plants and their hybrids is essential for an effective breeding programme. Traditional classification of cocoa varieties relies on the characterisation of agricultural traits at plant maturity. A rapid and reliable method is described, based on genotypic analysis. An efficient DNA isolation procedure was developed, yielding unsheared DNA of high purity. Two genetic fingerprinting techniques, RAPD and AFLP, were evaluated for their suitability in distinguishing cocoa varieties. RAPD analysis was unsatisfactory due to the low frequency of polymorphisms and poor reproducibility. AFLP was reliable in distinguishing phenotypically identical, known varieties of cocoa. Importantly, AFLP also revealed intra- and inter-varietal variation.Abbreviations: AFLP, amplified fragment length polymorphism; APS, ammonium persulphate; CTAB, hexadecyltrimethylammonium bromide; DEB, DNA extraction buffer; f.wt., fresh weight; NEB, nuclei extraction buffer; PMSF, phenylmethanesulphonyl fluoride; RAPD, random amplified polymorphic DNA; T4 PNK, Bacteriophage T4 polynucleotide kinase; Taq, Thermus aquaticus; TBE, tris-borate-EDTA; TEMED, NNNN tetramethylethylenediamine.     

Free sigma subunit of Bacillus subtilis RNA polymerase binds to DNA

Summary The affinity of Bacillus subtilis RNA polymerase and subunits to DNA was examined by a non-denaturing polyacrylamide slab gel electrophoresis method which made it possible to resolve DNA-bound and free subunits. The results revealed that subunit, but not subunit had a relatively high affinity for double stranded DNA. The subunit was bound maximally to super-coiled pGR1-3 plasmid DNA at a mass ratio of /DNA of 0.7. With B. subtilis double stranded linear DNA one subunit was bound per approximately 1,000 base pairs. The -DNA complex was sufficiently stable for isolation by a molecular gel filtration column. The subunit had much higher affinity for super-coiled than for linear pGR1-3 DNA or for linear double stranded or denatured DNA from B. subtilis, E. coli, and calf thymus. These results indicate that the free B. subtilis subunit, in contrast to the E. coli subunit, can bind by itself to DNA.     

Structural and functional properties of DNA polymerase delta from rabbit bone marrow

Summary DNA polymerase delta, the most recently described class of eukaryotic DNA polymerase, has been purified to apparent homogeneity from rabbit bone marrow. Unlike the previously known eukaryotic DNA polymerases, delta has a 3 to 5 exonuclease as an integral component of its 122 000 molecular weight, single polypeptide structure. Similar to the function with prokaryotic DNA polymerases, the 3 to 5 exonuclease assists DNA polymerase delta in maintaining the fidelity of DNA synthesis by excising misincorporated nucleotides. DNA polymerase delta and the longer known eukaryotic DNA polymerase alpha are similar in many features. Both are very sensitive to sulfhydryl inhibitors such as N-ethylmaliemide (NEM) and to the antibiotic aphidicolin. Such criteria distinguish alpha and delta from DNA polymerases beta and gamma. This has led to the conclusion that nuclear DNA replication, which is sensitive to NEM and aphidicolin, is carried out by DNA polymerase alpha. However, the similar sensitivity of delta to these reagents requires that the role of alpha and delta in nuclear DNA replication be further defined. In many features DNA polymerase delta is also similar to the viral induced DNA polymerases such as the Herpes simplex virus DNA polymerases which also have associated 3 to 5 exonuclease. Understanding of DNA synthesis and the mechanism of DNA replication fidelity in mammalian cells depends upon a further understanding of both DNA polymerases alpha and delta and the nature of the relationship they have to each other.     

"Nick translation" in Escherichia coli rep strains deficient in DNA polymerase I activities.

Summary Using X174 replicative form (RF) DNA as an in vivo probe, we have investigated the coordinated action of the 53 exonuclease and polymerase activities of DNA polymerase I in order to understand better its physiological role. We constructed double mutants containing the rep mutation (the replication of X174 RF does not occur in rep mutants) together with a mutation affecting DNA polymerase I, either polA12 or polA546ex. Using these mutants, which are believed to be thermosensitive in the polymerase function or the 53 exonuclease function respectively, we studied the kinetics of nick translation at the permissive and non-permissive temperatures in vivo. The substrate was the X174 replicative form DNA nicked by the X174 gene A protein. E. coli rep polA546ex gave the lowest rate of nick translation, although the ability to perform nick translation, at least as measured by our assay, was still present. E. coli rep polA12 showed a similar low rate at the non-permissive temperature but a rate close to the wildtype level at the permissive temperature. Formation of the parental replicative form molecule in either strain was affected little, even at the restrictive temperature. Our results suggest that DNA polymerase I may not play a major role in ongoing DNA replication.     

Translational arrest in hypoxic potato tubers is correlated with the aberrant association of elongation factor EF-1α with polysomes

Translation elongation factor EF-1 became stably associated with potato tuber polysomes at the onset of hypoxia, coincident with a sharp rise in lactate and decrease in tissue pH. This aberrant association of EF-1 with polysomes also occurred when aerobic tuber extracts were acidified in vitro. Upon resumption of protein synthesis, an increase in the steady-state levels of EF-1, and expression of an EF-1/GUS transgene was observed. These results indicate that translational arrest results from to the failure of EF-1 to dissociate from ribosomes during the elongation cycle, and that restoration of protein synthesis is coordinated with expression of EF-1.     

RNA polymerase subunit biosynthesis in Bacillus subtilis

Summary The relative rates of RNA polymerase biosynthesis in Bacillus subtilis has been examined under steady-state growth conditions. The synthesis of RNA polymerase subunits (, , , ) has been followed by subunit fractionation of immunoprecipitated [³H]-labelled samples on SDS-polyacrylamide gels. The stoichiometries of ::: subunits have been determined from cultures pulse-labelled during steady-state growth. The results suggest that an unassembled pool of the -subunit exists from which the holoenzyme is formed.Upon shift-up from acetate to glycerol containing medium, a rapid rise in the differential rate of core enzyme synthesis was observed, while the rate of synthesis of the -subunit was not stimulated. During shift-down, a concomitant reduction in the rate of synthesis of all subunits occurred for the first 20 min after the shift; thereafter, a rate of synthesis characteristic of the new growth rate was established.As cultures enter sporulation, an immediate reduction in the rate of -subunit synthesis was demonstrated.     

Stable transformation via electroporation into maize Type II callus and regeneration of fertile transgenic plants

Maize Type II callus tissue was used as the plant material for genetic transformation via electroporation. Plasmid DNA containing a selectable marker gene (either neomycin phosphotransferase (npt-II) or phosphinothricin acetyl transferase (bar)), and a screenable marker gene (gus A) was incubated with the tissue prior to electroporation. Electroporated callus tissue was placed on selection medium containing kanamycin sulfate or Bast. No kanamycin resistant colonies were recovered whereas four independent Basta resistant callus isolates were recovered from a total of 544 cuvettes electroporated. After 8 to 16 weeks on the Basta containing medium, selected calli were isolated and maintained in individual selection plates for 4 to 6 weeks until sufficient tissue accumulated. Enzyme assays and DNA analyses were performed to verify the transformation events. Several plants were regenerated from individual callus isolates. The plants derived from one callus isolate were male sterile while those derived from the other isolates were both male and female fertile. Most plants showed Basta resistance. DNA analyses confirmed the presence of the introduced bar gene(s) in the primary regenerants and their progeny. The integration patterns of the inserted DNA appeared to be complex.     

Phenotypic analyses of lymphokine-activated killer cells that release interferon γ and tumor necrosis factor α

Summary We recently reported that interleukin-2(IL-2)-activated peripheral blood lymphocytes and CD3⁺, lymphokine-activated killer (LAK) cell clones release tumor necrosis factor (TNF) and interferon (IFN) when stimulated with K562 erythroleukemia cells. We examined the phenotype of IL-2-activated peripheral blood leukocytes that secrete TNF and IFN when stimulated with K562 cells and demonstrated that TNF secretion is not due to the presence of contaminating mononuclear phagocytes. Further, we demonstrate that IL-2-activated natural killer (NK) cells release only IFN when stimulated with K562 cells while T lymphocytes exposed to monoclonal anti-CD3 and K562 cells secrete both TNF and IFN. However, T cells stimulated only with K562 cells did not release IFN or TNF while the admixture of these T cells with NK cells, when stimulated with K562 cells, released levels of TNF comparable to those produced by the unseparated cells. At present it is unclear whether only one or both effector cell types respond to K562 by releasing TNF or why the presence both cell types is needed.This work was supported by grants from the national Institutes of Health (CA 23074 and CA 17094) and the Arizona Disease Commission (8277-000000-1-0-YR-9301)     

Functional analysis of a complex oncogene arrangement in biotype III Agrobacterium tumefaciens strains

The ubiquitous grapevine-associated octopine/cucumopine Ti plasmids of biotype III Agrobacterium tumefaciens strains carry two T regions, TA and TB, with a complex oncogene arrangement. Within the octopine/cucumopine group, two main strain types were identified: large TA strains with a TA region resembling the TL region of the biotype I octopine strain Ach5 and small TA strains with a similar T region organization as the large TA strains but with a large internal TA deletion. Structural and functional studies of the representative large TA strain Tm4 revealed six oncogenes. Each oncogene was inserted in a disarmed vector and tested for biological activity using the corresponding oncogenes of Ach5 as standards. Five Tm4 oncogenes, TA-iaaM, T-ipt, T-6b, TB-iaaH and TB-iaaM, were shown to be active, the IS-interrupted TA-iaaH gene was inactive. To study the role of each gene in the pTiTm4 context, several single and multiple pTiTm4 mutations were constructed. It was shown that whereas TA-iaaM and TB-iaaH are essential for tumour formation on grapevine, T-ipt, T-6b and TB-iaaM are not. The avirulence of the TA-iaaM ^- mutant was shown to be due to an inhibitory effect of the T-ipt gene, since a TA-iaaM ^- /T-ipt ^- double mutant was fully virulent. We conclude that the TA-iaaM gene of large TA strains is specifically required to counteract the tumour growth inhibiting activity of the T-ipt gene. Both TA-iaaM and T-ipt are absent from the small TA strains. A model on the roles and interactions of the different oncogenes in large TA and small TA strains is presented.     

Different binding of RNA polymerase to individual promoters

Summary The amount of E. coli RNA polymerase which can be bound to individual promoters on pgal and dgal phage DNA in a stable heparin-resistant form was measured by assessing its capacity to transcribe, upon addition of the nucleoside triphosphates, the RNA sequences starting at these promoters. These RNA species were analysed by competition hybridization to separated single strands of , pgal and dgal phage DNA.Individual promoters bind, at saturation, different numbers of polymerase molecules. From the amount of polymerase necessary to saturate all promoters (Fig. 3), from the proportions of RNA synthesized at the individual promoters (Table 1) and from the amounts of -³²P-ATP or-GTP label incorporated into the different RNA species (Tables 2 and 3) we calculate polymerase storage capacities for the promoters as follows: gal: 6 molecules; l-strand specific: 3–5 molecules starting with ATP and 1 molecule starting with GTP; r-strand specific: 3–5 molecules starting with ATP (and perhaps one molecule starting with GTP); these estimates are lower limits and may be too small by a factor of up to three.The heparin resistant binding of six polymerase molecules to the gal promoter is dependent on CGA protein and cAMP, but ATP and GTP can allow one polymerase to bind to the same site or to a very close one.Several parameters of polymerase binding are different with the individual promoters tested.     

The major DNA polymerase in cultured plant cells: Partial purification and correlation with cell multiplication

A DNA polymerase activity was isolated from cells of Oryza sativa L. grown in suspension culture. Molecular mass ( 180,000), optimal requirements for pH (neutral), Mg²⁺ (5–10 mM), Mn²⁺ (1 mM), template preference (activated DNA), lack of activity with native or denatured DNA, and sensitivity to N-ethylmaleimide and ionic strength are similar to those of the vertebrate -polymerase. Like DNA polymerase , the DNA polymerase described in this work is the most abundant in proliferating cells of Oryza sativa L., Parthenocissus tricuspidata (Siebold et Zucc.) Planchon, Acer pseudoplatanus L., and Medicago sativa L. and responds to changes in the rate of cell multiplication. We therefore postulate that this -like DNA polymerase is the replicating enzyme of plant cells.Abbreviations BSA bovine serum albumin - EDTA ethylendiamino-tetracetic acid - DTT dithiothreitol - PTSF p-toluenesulfonyl fluoride     

Effect of α-amanitine on puffing and intranuclear RNA synthesis in Chironomus salivary glands

Incubation of Chironomus salivary glands with -amanitine in concentrations from 1 to 10 /ml results in the suppression of puffing and chromosomal ³H-uridine incorporation after 30 to 60 min in 80% of the cells. Nucleolar ³H-uridine incorporation remains completely unaffected. Even 4 h after the injection of high doses of -amanitine into living larvae, nucleolar incorporation is still pronounced. The distribution of resistant cells within the salivary glands suggests that the uptake of -amanitine is subject to physiological restrictions.—A puff typically induced during in vitro incubation of salivary glands was found to be less sensitive to -amanitine than the Balbiani rings.     

Purification and characterization of the 5′ → 3′ exonuclease domain-deleted Thermus filiformis DNA polymerase expressed in Escherichia coli

The gene encoding 5 3 exonuclease domain-deleted Tfi DNA polymerase, named 5 3 Exo^– Tfi fragment, from Thermus filiformis was expressed in Escherichia coli under the control of the tac promoter on a high-copy plasmid, pJR. The expressed enzyme was purified 27-fold with a 19% yield and a specific activity of 2621 U mg^–1 protein. The 5 3 exonuclease domain of Tfi DNA polymerase was removed without significant effect on enzyme activity and stability. PCR conditions for the 5 3 Exo^– Tfi fragment were more tolerant to the buffer composition as compared to the full-length enzyme.     

Feedback regulation of RNA polymerase subunit synthesis after the conditional overproduction of RNA polymerase in Escherichia coli

Summary The and subunit of RNA polymerase are thought to be controlled by a translational feedback mechanism regulated by the concentration of RNA polymerase holoenzyme. To study this regulation in vivo, an inducible RNA polymerase overproduction system was developed. This system utilizes plasmids from two incompatibility groups that carry RNA polymerase subunit genes under lac promoter/operator control. When the structural genes encoding the components of core RNA polymerase (, and ) or holoenzyme (, , and ⁷⁰) are present on the plasmids, induction of the lac promoter results in a two fold increase in the concentration of functional RNA polymerase. The induction of RNA polymerase overproduction is characterized by an initial large burst of synthesis followed by a gradual decrease as the concentration of RNA polymerase increases. Overproduction of RNA polymerase in a strain carrying an electrophoretic mobility mutation in the rpoB gene results in the specific repression of synthesis off the chromosome. These results indicate that RNA polymerase feedback regulation controls synthesis in vivo.     

The underwater light field in the Bellingshausen and Amundsen Seas (Antarctica)

The underwater light field in the Bellingshausen andAdmundsen Seas was characterised using data collectedduring the R/V Polarstern cruise ANT XI/3, from12.1.94 to 27.3.94. The euphotic zone varied from 24to 100 m depth. Spectral diffuse vertical attenuationcoefficients (K _d ())were determined for 12narrow wavebands as well as for photosyntheticallyavailable radiation (PAR, 400–700 nm): K _d (490)ranged from 0.03 to 0.26 m¹; K _d (550) from0.04 to 0.17 m¹; K _d (683) from 0.04 to0.17 m¹; and K _d (PAR) varied from 0.02 to0.25 m¹. K _d () for wavelengths centred at412 nm, 443 nm, 465 nm, 490 nm, 510 nm, 520 nm and550 nm were significantly correlated with chlorophyllconcentration (ranging from 0.1 to 6 mg m³). Thevertical attenuation coefficients for 340 nm and380 nm ranged from 0.10 to 0.69 m¹ and from 0.05to 0.34 m¹, respectively, and were also highlycorrelated with chlorophyll concentrations. These K _d values indicate that the 1% penetration depthmay reach maxima of 46 m and 92 m for 340 nm and380 nm, respectively. The spectral radiancereflectances (Rr()) for 443 nm, 510 nm and 550 nmwere less than 0.01 sr¹. Rr() for 665 nm and683 nm increased with depth up to 0.2 sr¹ because ofchlorophyll fluorescence. Using a model that predicts downwardirradiances by taking into account the attenuation bywater and absorption by chlorophyll, we show thatchlorophyll fluorescence has a significant influenceon the red downward irradiance (E _d (633, 665, 683))in deeper layers. The ability of the phytoplanktonpopulation to influence the light environment byautofluorescence and absorption processes depends onthe light conditions and on the photoacclimation ofthe cells, represented by the in vivo crosssection absorption coefficient of chlorophyll (a*). Theobtained mean chlorophyll-specific light attenuationcoefficients of phytoplankton in situ (k _d ) are higherthan the in vivo absorption coefficient of chlorophyll,more than to be excepted from the scattering. a*(), m² mg chl¹, decreased due topackaging effect with increasing chlorophyllconcentrations.     

A mutant of Escherichia coli K12 deficient in the 5''-3'' exonucleolytic activity of DNA polymerase I. II. Purification and properties of the mutant enzyme

Summary The enzymatic properties of purified DNA polymerase I from a strain of Escherichia coli K12 with a mutation in the polA gene have been studied. The polymerizing activity of the mutant enzyme is similar to that of the enzyme from isogenic wild-type cells, when the activity is measured on exonuclease III treated calf-thymus DNA. Also the 3–5 exonucleolytic activity is not significantly different for both enzyme preparations. The 5–3 exonucleolytic activity of DNA polymerase I isolated from the mutant strain, however, is much lower than that of wild-type DNA polymerase I. The products formed by the action of the wild-type and the mutant enzyme on nicked circular double-stranded DNA of phage X174 (RFII DNA) were analysed by sucrose-gradient sedimentation and electron-microscopy. When RFII DNA was incubated with wild-type enzyme 80% of the molecules were converted into linear molecules. All linear molecules were shorter than one phage genome. Only 25% of the molecules were branched. After incubation of RFII DNA with the mutant enzyme 62% of the molecules have become linear. More than 90% of these linear molecules were branched and the majority of them was longer than one phage genome.     

‘Enteroglucagon’: A specific effect on gastric glands isolated from the rat fundus. Evidence for an ‘oxyntomodulin’ action

A newly isolated porcine glucagon-like biologically active intestinal peptide (enteroglucagon) has been tested for its ability to stimulate the cyclic AMP system present in different tissue preparations from the rat: membranes prepared from liver or from isolated fundic glands as well as intact glands isolated from either the fundus or the antrum. Enteroglucagon (EG) was about l0 times less potent than pancreatic glucagon (G) in liver membranes, whereas it was about 20 times more potent than G in fundic membranes as well as in fundic glands, where it acts at doses as low as 3 × 10^-10 M. EG and G were practically ineffective in antral glands. It is concluded that EG is an under-glucagon in rat liver, whereas it is a super-glucagon in rat fundic glands. Accordingly, we propose to call this peptide 'oxyntomodulin'.     

Purification and characterization of DNA polymerase alpha of chinese hamster ovary cells

Summary The major pol activity of CHO cells was purified 2 800-fold to near homogeneity and was characterized with respect to its physical and catalytic properties. The purified enzyme, upon analysis in denaturing activity gels, displayed a major, 120 kilodalton, catalytically active core and two minor, catalytically inactive components of 180 and 135 kilodaltons. The native form of the enzyme behaved in velocity sedimentation and gel permeation experiments as an asymmetric protein of an apparent Mr. of 515 kilodaltons. The purified enzyme displayed catalytic behavior and inhibitor sensitivity typical of that displayed by other mammalian pol alphas. Specifically, the enzyme: (1) was sensitive to n-ethylmaleimide and the pol -specific inhibitors, BuPdGTP and aphidicolin; (2) was subject to neutralization by specific monoclonal antibodies raised against human pol ; (3) was devoid of detectable 3 to 5 exonuclease activity, and (4) displayed a ribonucleotide-dependent DNA primase activity.     

The Correcting Role of Autonomous 3" →="" 5"="" exonucleases="" contained="" in="" mammalian="" multienzyme="" dna="" polymerase="" complexes"="

A study was made of the correcting role of autonomous 3" 5" exonucleases (AE) contained in multienzyme DNA polymerase complexes of rat hepatocytes or calf thymocytes. DNA was synthesized on phage X174 amber3 or M13mp2 primer–templates, and used to transfect Escherichia coli spheroplasts. Frequencies were estimated for direct and reverse mutations resulting from mistakes made in the course of in vitro DNA synthesis. The error rate of the hepatocyte complex was estimated at 3·10^–6 with equimolar dNTP, and increased tenfold when proteins accounting for 70% of the total 3" 5" exonuclease activity of the complex were removed. The fidelity of DNA synthesis was completely restored in the presence of exogenous AE ( subunit of E. coli DNA polymerase III). Nuclear (Pol _n) and cytosolic (Pol _c) forms of DNA polymerase were isolated from calf thymocytes. The former was shown to contain an AE (TREX2) absent from the latter. As compared with Pol _c, Pol _n had a 20-fold higher exo/pol ratio and allowed 4–5 times higher fidelity of DNA synthesis. The error rate of DNA polymerase complexes changed when dNTP were used in nonequimolar amounts.     

ColE plasmid replication in DNA polymerase I-deficient strains ofEscherichia coli

Summary Replication of the non-conjugative plasmids ColE1, ColE2 and ColE3 has been examined in a number of DNA polymerase I-deficient strains, two of which contain the amber mutationpolA1 along with either of two temperature-sensitivesupF amber suppressors. These latter two strains produce reduced amounts of DNA polymerase I polymerizing activity of similar, if not identical properties to that produced bypolA⁺ strains. Our results indicate that the ColE plasmids require different amounts of DNA polymerase I for stable plasmid maintenance. Moreover whereas all three plasmids are maintained in a strain defective in the 53 exonuclease activity of DNA polymerase I, ColE2 and ColE3 are not stably maintained between 30° and 43° in a number of DNA polymerase I-deficient strains that are temperature-sensitive for ColE1 replication.