Enhancing PCR amplification and sequencing using DNA-binding proteins

The polymerase chain reaction (PCR) is a powerful core molecular biology technique, which when coupled to chain termination sequencing allows gene and DNA sequence information to be derived rapidly. A number of modifications to the basic PCR format have been developed in an attempt to increase amplification efficiency and the specificity of the reaction. We have applied the use of DNA-binding protein, gene 32 protein from bacteriophage T4 (T4gp32) to increase amplification efficiency with a number of diverse templates. In addition, we have found that using single-stranded DNA-binding protein (SSB) or recA protein in DNA sequencing reactions dramatically increases the resolution of sequencing runs. The use of DNA-binding proteins in amplification and sequencing may prove to be generally applicable in improving the yield and quality of a number of templates from various sources.     

Leptospira genomes are modified at 5'-GTAC.

Genomic DNAs of 14 strains from seven species of the spirochete Leptospira were resistant to cleavage by the restriction endonuclease RsaI (5'-GTAC). A modified base comigrating with m4C was detected by chromatography. Genomic DNAs from other spirochetes, Borrelia group VS461, and Serpulina strains were not resistant to RsaI digestion. Modification at 5'-GTAm4C may occur in most or all strains of all species of Leptospira but not in all genera of spirochetes. Genus-wide DNA modification has rarely been observed in bacteria.     

INFLUENCE OF NATURAL ULTRAVIOLET RADIATION ON LOTIC PERIPHYTIC DIATOM COMMUNITY GROWTH,BIOMASS ACCRUAL,AND SPECIES COMPOSITION: SHORT-TERM VERSUS LONG-TERM EFFECTS1, 2

Growth rates, accumulation dynamics, and species succession of periphytic diatom communities were examined in the presence and absence of natural ultraviolet (UV) radiation using a series of outdoor, continuous-flow experimental flumes located on the South Thompson River, British Columbia. In a short-term experiment (2–3 wk), log-phase growth rates of naturally seeded diatom communities comprised of Tabellaria fenestrata (Lyngb.) Kütz., T. flocculosa (Roth) Kütz., Fragilaria crotonesis Kitton, and F. vaucheriae (Ehr.) Peter. exposed to 90% ambient photosynthetically active radiation (PAR) + UV were 30–40% lower than growth rates under 90% PAR alone. UV inhibition of growth rate was independent of the degree of P limitation within the range of relative specific growth rates (μ:μ_max-P) of 0.5–1.0. In a long-term trial, inhibition of attached diatom accumulation under 90% PAR + UV during the first 2–3 wk was corroborated. Reduction of full sunlight to 50% PAR + UV prevented the initial inhibition phase. The initial inihibitory effect of 90% PAR + UV on algal accumulation was reversed after 3–4 wk, and by 5 wk total diatom abundance (chlorophyll a, cell numbers and cell biovolumes) in communities exposed to PAR + UV were 2–4-old greater than in communities protected from UV. Under 90% PAR + UV and 50% PAR + UV, a succession to stalked diatom genera (Cymbella and Gomphoneis) occurred. Species succession under UV radiation doubled the mean cell size of the diatom communities. The shift from inhibition to a long-term increase in the autotrophic community under PAR + UV compared to PAR alone provides further evidence against the use of short-term incubation experiments to define the long-term implications of increases in UVB. These results suggest that the ecological effects of present-day levels of UVB and UVB:UVA ratios on autotrophic communities are not well understood and might be mediated through complex trophic level interactions.     

ANTIVIRAL ACTIVITY OF CULTURED BLUE-GREEN ALGAE (CYANOPHYTA)1

Lipophilic and hydrophilic extracts from approximately 600 strains of cultured cyanophytes, representing some 300 species, were examined for antiviral activity against three pathogenic viruses. Approximately 10% of the cultures produced substances that caused significant reduction in cytopathic effect normally associated with viral infection. The screening program identified the order Chroococcales as commonly producing antiviral agents.     

GENOTYPIC VARIATION AND ALTERNATING DNA LEVELS AT CONSTANT CHROMOSOME NUMBERS IN THE LIFE HISTORY OF THE BROWN ALGA HAPLOSPORA GLOBOSA (TILOPTERIDALES)1

The brown algal order Tilopteridales contains three monospecific genera with reduced life histories, Which are assumed to have been derived form ancestors with oogamous reproduction and alternation of generations. The Newfoundland population of Haplospora globosa Kjellman still shows an alternation of gametophytes and sporophytes, but the chromosome Numbers remain equal because of parthenogenesis and apomeiosis, However, DNA fluorometry showed that the DNA level is twice as high in the Sporophytes as in the gametophytes, The DNA variation at constant chromosome numbers is presumably due to endomitosis combined with a law degree of polyteny. A genotypic variant of Haplospora is represented by the population at Helgoland (F.R.G.) where only sporophytes exist, Spores develop into sporophytes instead of gametophytes, and the plants have reduced chromosome number but the same DNA level as the Newfoundland sporophytes     

Species of Borrelia distinguished by restriction site polymorphisms in 16S rRNA genes

Abstract Three phyletic groups of Borrelia associated with Lyme disease, B. burgdorferi, B. garinii and group VS461 can be distinguished from each other and other species of Borrelia by Bfa I restriction site polymorphisms in PCR amplified 16S rRNA genes. One strain isolated from an Ixodes pacificus tick in California that was previously unclassifiable was distinguishable from B. burgdorferi by an Mnl I restriction site polymorphism.     

Regulation of expression of the 3β-hydroxysteroid dehydrogenases of human placenta and fetal adrenal

The appropriate expression of 3β-hydroxysteroid dehydrogenase/Δ^5→4-isomerase (3β-HSD) is vital for mammalian reproduction, fetal growth and life maintenance. Several isoforms of 3β-HSD, the products of separate genes, have been identified in various species including man. Current investigations are targeted toward defining the processes that regulate the levels of specific isoforms in various steroidogenic tissues of man. High levels of expression of 3β-HSD were observed in placental tissues. It has been generally considered that the multinucleated syncytiotrophoblastic cells are the principal sites of 3β-HSD expression and, moreover, that 3β-HSD expression is intimately associated with cyclic AMP-promoted formation of syncytia. Herein we report the presence of 3β-HSD immunoreactive and mRNA species in uninucleate cytotrophoblasts in the chorion laeve, similar to that in syncytia but not cytotrophoblast placenta. In vitro, 3β-HSD levels in chorion laeve cytotrophoblasts were not increased with time nor after treatment with adenylate cyclase activators, whereas villous cytotrophoblasts spontaneously demonstrated progressive, increased 3β-HSD expression. Moreover, 3β-HSD synthesis appeared to precede morphologic syncytial formation. Thus high steroidogenic enzyme expression in placenta is not necessarily closely linked to formation of syncytia. Both Western immunoblot and enzymic activity analyses also indicated that the 3β-HSD expressed in these cytotrophoblastic populations was the 3β-HSD type I gene product (M_r, 45K) and not 3β-HSD type II (M_r, 44K) expressed in fetal testis. In cultures of fetal zone and definitive zone cell of human fetal adrenal, 3β-HSD expression was not detected until ACTH was added. ACTH, likely acting in a cyclic AMP-dependent process, induced 3β-HSD type II activity and mRNA expression. The higher level of 3β-HSD mRNA in definitive zone compared with fetal zone cells was associated with parallel increases in cortisol secretion relative to dehydroepiandrosterone sulfate formation.     

ANALYSIS OF POLYPEPTIDES ASSOCIATED WITH SHOOT FORMATION IN TOBACCO CALLUS CULTURES

Callus lines of Nicotiana tabacum were selected for competence and lack of competence in shoot formation. Changes in total and chromosomal polypeptides in these shoot-forming and nonshoot-forming tobacco cultures were examined by twodimensional polyacrylamide gel electrophoresis. Qualitative and quantitative differences in total, nonhistone chromosomal, and basic chromosomal polypeptides were evident throughout the 7-d test period. The analysis of total proteins identified polypeptides specific to shoot-forming and nonshoot-forming tissue during the 7-d sampling period. A small number of basic chromosomal proteins were found solely in shoot-forming or nonshoot-forming tissue. One basic chromosomal protein was detected in only nonshoot-forming tissue at all sampling times. Two proteins, although present in shoot-forming tissue, were present at elevated levels in the nonshoot-forming cultures. No temporal changes in basic proteins over the 7-d incubation period were observed. Qualitative differences in total nonhistone chromosomal polypeptides in the shoot-forming and nonshoot-forming tissue were also observed. Differences in chromosomal polypeptides were observed. In contrast to the basic chromosomal proteins, temporal variation in the nonhistone chromosomal polypeptides was demonstrated. Throughout the 7-d sampling period, 29 and 12 nonhistone chromosomal polypeptides varied qualitatively in shoot-forming and nonshoot-forming callus cultures, respectively. In vitro labeling with ³²P-orthophosphate indicated that approximately 1.0% and 0.3% of the nonhistone chromosomal proteins were phosphorylated in the shoot-forming and nonshoot-forming cultures. Of these phosphorylated polypeptides, one was present in nonshoot-forming tissue and three were detected only in the shoot-forming tissue. Phosphorylation occurred at serine or threonine residues.