The importance of fixation procedures on DNA template and its suitability for solution-phase polymerase chain reaction and PCR in situ hybridization

Summary Conventional solution-phase polymerase chain reaction (PCR) and in situ PCR/PCR in situ hybridization are powerful tools for retrospective analysis of fixed paraffin wax-embedded material. Amplification failure using these techniques is now encountered in some centres using archival fixed tissues. Such ailures may not only be due to absent target DNA sequences in the tissues, but may be a direct effect of the type of fixative, fixation time and/or fixation temperature used. The type of nucleic acid extraction procedure applied will also influence amplification results. This is particularly true with in situ PCR/PCR in situ hybridization.To examine these effects in solution-phase PCR, -globin gene was amplified in 100 mg pieces of tonsillar tissue fixed in Formal saline, 10% formalin, neutral buffered formaldehyde, Carnoy's, Bouin's, buffered formaldehyde sublimate, Zenker's, Helly's and glutaraldehyde at 0 to 4°C, room temperature and 37°C fixation temperatures and for fixation periods of 6, 24, 48 and 72 hours and 1 week. DNA extraction procedures used were simple boiling and 5 days' proteinase K digestion at 37°C. Amplified product was visible primarily yet variably from tissue fixed in neutral buffered formaldehyde and Carnoy's, whereas fixation in mercuric chloride-based fixatives produced consistently negative results. Room temperature and 37°C fixation temperature appeared most conducive to yielding amplifiable DNA template. Fixation times of 24 and 48 hours in neutral buffered formaldehyde and Carnoy's again favoured amplification.Fixed SiHa cells (containing 1–2 copies of HPV 16) were examined using PCR in situ hybridization for the amplification of HPV 16. Discrete and diffuse amplification signals were obtained. Neutral buffered formaldehyde fixation for 12–24 hours yielded amplifiable material suitable for use with PCR in situ hybridization. Overall amplification success within cellular preparations was 40%, with non-specific background staining also seen. Possible technical problems encountered with PCR in situ hybridization are discussed.     

Continuous production of glucoamylase by immobilized growing cells ofAureobasidium pullulans

Summary Yeast-like cells ofAureobasidium pullulans were immobilized in Ca-alginate gel beads and employed for continuous production of glucoamylase in a fluidized-bed reactor (250 ml working volume). After an activation time of 48 h, to allow the in situ germination of the fungal blastospores, the reactor was operated continuously for over 150 h. A steady state enzyme concentration of 1.2–1.3 U ml^–1 of glucoamylase activity and an enzyme volumetric productivity of ca. 130 U ml^–1 h^–1 were obtained at a medium flow rate of 26 ml h^–1. Enzyme activity and volumetric productivity were influenced by fermentation conditions such as inoculum size and airflow rate.     

Comparison of photobioreactors for cultivation of Undaria pinnatifida gametophytes

Undaria pinnatifida gametophytes were grown in 2.5 l bubble column and airlift reactor at 25 °C and light intensity of 40 mol m^–2 s^–1 for 6 days. With aeration at 1 l min^–1, the airlift reactor yielded higher growth rate (0.12 mg DW ml^–1 d^–1) than a bubble column (0.08 mg DW ml^–1 d^–1). The advantages were related to the more homogeneous fluid dynamic characteristics of the airlift reactor.     

Enhancement of production of cloned α-amylase by lactic acid feeding from recombinant Saccharomyces cerevisiae using a SUC2 promoter

-Amylase production was higher (13 units ml^–1) when a recombinant Saccharomyces cerevisiae containing a SUC2 promoter was grown with 10 g lactic acid l^–1 than without addition (8 units ml^–1). With continuous lactic acid feeding in the inducing phase, -amylase increased to 79 units ml^–1 in a 1-l jar fermenter.     

Quantification of the contribution of surface outgrowth to biocatalysis in sol-gels: oxytetracycline production by <Emphasis Type="Italic">Streptomyces rimosus</Emphasis>

A technique was developed for differentiating the activity of microbes solely within sol gels by using the contribution of biomass outgrowth. Streptomyces rimosus was immobilised in colloidal silica gels and biomass growth, oxytetracycline synthesis, pH and carbohydrate consumption were compared for UV surface-sterilised gels, untreated gels, and liquid cultures. Absolute and biomass specific oxytetracycline yields were higher for non-sterile gels than for liquid culture. Biomass solely within colloidal silica gels (1.7 mg ml^–1), and gels obtained from colloidal silica modified by addition of larger silica particles (1.2 mg ml^–1) yielded 27 and 21 g ml^–1 oxytetracycline compared with 97 and 104 g ml^–1 for unsterilised gels (3.6 and 5.2 mg ml^–1 biomass) displaying outgrowth. It was therefore apparent that biomass and antibiotic production within the gels was limited and that optimisation requires gel modification.     

Phenotypic expression of Vogesella indigofera upon exposure to hexavalent chromium,Cr6+

A eubacterium producing a blue pigment was isolated from a drinking water filter, and subsequently identified as Vogesella indigofera. This bacterium was further investigated for its morphological and biochemical characteristics after exposure to hexavalent chromium, Cr⁶⁺. The threshold Cr⁶⁺ concentration inhibiting the pigment production by V. indigofera was 200–300 g ml^–1 in liquid cultures of nutrient broth and 100–150 g ml^–1 on nutrient agar plates. The Cr⁶⁺ concentration preventing V. indigofera growth was 300–400 g ml^–1 in liquid cultures, but greater than 150 g ml^–1 on agar plates. Moreover, rugose colonies without the blue pigmentation were observed on agar plates amended with 150 (g Cr⁶⁺) ml^–1. The biochemical utilization profiles of the colonies without pigmentation did not differ from the original pigment-producing ones, indicating phenotypic plasticity of this bacterium. The difference of phenotypic expression of V. indigofera under various Cr⁶⁺ concentrations might have potential application as a pollution bioindicator for heavy metals.     

Tomato extensin and extensin-like cDNAs: structure and expression in response to wounding

Two tomato cDNA libraries were synthesized from poly(A)⁺ RNAs isolated from unwounded and wounded tomato stems. These cDNA libraries were packaged in gt10 and screened by in situ plaque hybridization with a tomato extensin gene clone (pTom 5.10). Several cDNA clones were identified and isolated from both libraries in this manner and subjected to restriction enzyme digestion, Southern gel blot hybridization, RNA gel blot hybridization, and DNA sequence analyses. From these analyses, the various cDNA clones were found to fall into one of five distinct classes (classes I–V). Class I clones hybridized to a 4.0 kb mRNA which accumulated markedly after wounding and encoded an extensin characterized largely by Ser-(Pro)₄-Ser-Pro-Ser-(Pro)₄-(Tyr)₃-Lys repeats. Class II clones hybridized to a 2.6 kb mRNA which showed no accumulation following wounding and encoded an extensin containing Ser-(Pro)₄-Ser-Pro-Ser-(Pro)₄-Thr-(Tyr)_1–3-Ser repeats. Class III clones hybridized to a 0.6 kb mRNA which greatly accumulated in response to wounding and encoded a glycine-rich protein (GRP) with (Gly)_2–6-Tyr-Pro and(Gly)_2–6-Arg repeats. Class IV clones contained both class I and class III DNA sequences and consequently hybridized to both the 4.0 kb and the 0.6 kb wound-accumulating mRNAs; these clones encoded a portion of a GRP sequence on one DNA strand and encoded a portion of an extensin sequence on the other DNA strand. Class V clones hybridized to a 2.3 kb mRNA which decreased following wounding and encoded a GRP sequence characterized by (Gly)_2–5-Arg repeats.     

A one-day double-labelling technique for tissue specimens: Immunogold-silver staining forin situ hybridization combined with alkaline phosphatase-anti-alkaline phosphatase (APAAP) immunohistochemistry for antigens

Summary An improved technique is described that addresses the problems of sensitivity, specificity, the use of hazardous radioactive equipment and time consumption in immunohistochemical labelling and double labelling ofin situ hybridization of tissue specimens. It consists of a two-step protocol in which digoxigenin-uridine triphosphate (UTP) labelled riboprobes in thein situ hybridization step are visualized by the immunogold-silver staining method, and double labelling of tissue antigens is achieved by the application of an alkaline phosphatase-anti-alkaline phosphatase staining step. We tested this protocol using snap-frozen tissue sections of synovial tissue from patients with rheumatoid arthritis. The target mRNA was detected by perforin or cathepsin D riboprobes, the double labelling was performed using anti-collagen type IV and alpha-smooth muscle actin antibodies. It is concluded that, in comparison with an established three-to four-day double-labelling protocol used in many laboratories, this one-day combination is currently the most rapid assay of reliable quality for double labelling ofin situ hybridization products and tissue antigens.     

The relative importance of different ciliate taxa in the pelagic food web of lake constance

Abundance, biovolume, and species composition of pelagic ciliates in Lake Constance were recorded over two annual cycles (1987/88). Production was estimated from mean annual biovolumes and size-specific growth rates obtained from the literature. Cell concentrations and biovolumes ranged from 0.1 to 120 cells ml^–1 and from 3 to 1,200 mm³ m^–3, respectively. Mean annual values were, respectively, 6.8 cells ml^–1 and 94 mm³ m^–3 in 1987, and 12.0 cells ml^–1 and 130 mm³ m^–3 in 1988. In both years, prostome nanociliates (<20m) dominated numerically, while strobiliids in the size range 20–35m contributed most significantly to ciliate production. Ciliate community production, according to a crude calculation, yielded approximately 10–15 g C m^–2 year^–1.     

Nitrogen fixation by Nodularia spumigena Mertens (Cyanobacteriaceae). 2: Laboratory studies

The effects of changes in diurnal light patterns, salinity, and phosphorus on nitrogen fixation (as measured by acetylene reduction) by Nodularia spumigena Mertens were examined. As well, the effects of added inorganic nitrogen on growth, nitrogen fixation and heterocyt frequencies, and changes in nitrogen fixation and heterocyst frequencies during the growth cycle of Nodularia in cultures were determined.The diurnal pattern of nitrogenase activity in Nodularia was primarily light-induced, though dark activity did occur. Nitrogenase activity following a period of darkness exceeded the normal light rate (> 90 compared to 50 nmol · C₂H₂ reduced · ml^–1 · h^–1). Nitrogen fixation was reduced by high and very low salinities (5 to 10 was the optimum range), and added phosphorus stimulated nitrogenase in P-starved cells. Added nitrogen (ammonium or nitrate) had no effect on the growth of Nodularia, but in short term studies, ammonium completely inhibited nitrogenase activity. Heterocyst frequencies were greatest in the log phase of growth (to 40 per mm). During stationary phase, nitrogenase activity was negligable.     

Strain improvement ofArthrobacter simplex by protoplast fusion

Anl-tryptophan auxotroph and milky mutants were derived from an inducible cholesterol oxidase-producing bacterium,Arthrobacter simplex USA18, via UV-mutagenesis. Protoplasts of these mutants and a constitutive cholesterol oxidase producer, strain US3011, were prepared by growing cells in the presence of ampicillin (20g ml^–1) followed by digestion with lysozyme. Protoplast fusion between tested strains with complementary characteristics was achieved in the presence of 20–40% polyethylene glycol 6000. The fusion frequency was about 1.5–1.7×10^–3. The cholesterol oxidase activity of four fusants in a cholesterol-containing medium was 20–60% higher than that of parental strains. This study demonstrated that protoplast fusion is applicable to strain improvement ofArthrobacter strains for enzyme production.     

Thermostable cellulases from <Emphasis Type="Italic">Streptomyces</Emphasis>sp.: scale-up production in a 50-l fermenter

Thermostable cellulase was produced by Streptomyces sp. T3-1 grown in a 50-l fermenter. Maximum cellulase activity was attained on the fourth day when agitation speeds and aeration rates were controlled at 300 rpm and 0.75 vvm, respectively. Maximum enzyme activities were: 148 IU CMCase ml^–1, 45 IU Avicelase ml^–1, and 137 IU -glucosidase ml^–1 with productivity of 326 IU l^–1 h^–1, which were 10--32% higher than the values obtained in shake-flask culturesRevisions requested 12 October 2004/1 November 2004; Received received 1 November 2004/14 December 2004     

Accumulation of cadmium by immobilizedZoogloea ramigera 115

Summary Zoogloea ramigera 115 was immobilized into beads of calcium-alginate and placed into batch air-bubbled column reactors. In the absence of any added nutrients the immobilized bacterium adsorbed Cd from solutions containing levels of 2 and 20 g ml^–1 per day, over a period of 21 and 20 days, respectively. Adsorption of Cd from solutions containing 20 g ml^–1 Cd was better than 90% for 16 days. Beads treated with Cd at 2 g ml^–1 never adsorbed less than 95% of the metal. Alginate adsorbed Cd as well, but inclusion of cells changed the effectiveness of adsorption. Of a 250 g ml^–1 Cd solution, alginate adsorbed 70.4% Cd in 60 min whereas alginate plus cells adsorbed 90.5% in the same time span. Temperature had no effect on adsorption by immobilized cells at levels of 2 and 10 g ml^–1 Cd. However at higher concentrations, binding was enhanced as temperature increased.Z. ramigera beads were stable during all treatments and for prolonged periods of time (21 days).     

Phloem bleeding from legume fruits—A technique for study of fruit nutrition

Summary Bleeding from phloem of cut distal tips of attached fruits was demonstrated in the genera Spartium, Genista, Lupinus and Jacksonia. Bleeding occurred over a 2–25 min period enabling 0.5–10 l of sap to be collected from a fruit. A detailed study of Lupinus albus L. showed that exudation rate declined exponentially after cutting, but without any change with time in solute levels in exudate. Bleeding resumed at its initial rate and solute concentration on recutting the fruit tip.Phloem exudates had a high pH (7.8-8.0), a sucrose content of 100–210 mg ml^-1 but only traces of monosaccharides. Surrounding pod tissues contained only 15–35 mg ml^-1 of sugars (tissue water basis) more than two thirds of this monosaccharide. Amino compounds were present in phloem exudates at 8–28 mg ml^-1, asparagine and glutamine predominating but a wide spectrum of other amino acids being also present. No significant differences in levels of organic solutes were observed in phloem exudates collected from tips of attached versus detached fruits, from phloem exudates collected from fruit tips versus pedicels, or from basal versus distal ends of a detached fruit.Potassium was the major cation (1.5–2.2 mg ml^-1) of the phloem exudate, Ca²⁺ was at a much lower level than either Mg²⁺ or Na⁺. Trace element levels in phloem exudates appeared to be influenced by availability to the plant from the rooting medium. Nitrate was absent though detectable in non-vascular tissues of the shoot. ¹⁴C- labelled assimilates were detected in exudates of L. albus one hour after feeding a source leaf ¹⁴CO₂; sucrose, organic acids and certain amino compounds achieved high specific labelling. ¹⁴CO₂ feeding studies coupled with the phloem bleeding technique revealed highly specific source-sink relationships between foliar organs and fruits of the primary inflorescence.     

In situ hybridization of “Nick-translated” 3H-ribosomal DNA to chromosomes from salamanders

A technique is described for preparation of ³H-labelled DNA by nick-translation employing deoxyribonuclease I and DNA polymerase I. The labelled DNA can be obtained in high yield with specific activities of 10⁶ cpm/g or more. Ribosomal DNA, isolated from ovaries of young Xenopus laevis, and whole DNA from Plethodon cinereus were labelled in this way. The rDNA was used for in situ hybridization to meiotic chromosomes from P. cinereus, P. vehiculum and P. dunni. Autoradiographs of in situ hybrids were exposed for 5 to 10 days, by which time nucleolus organizer regions on the chromosomes of all 3 species were clearly and specifically labelled. In all eases, labelling was confined to a short region near the middle of the short arm of both halves of a medium length bivalent. It is concluded that nick-translation is a useful and altogether efficient method of labelling nucleic acids for subsequent use in experiments involving in situ hybridizations.     

Insecticidal activity of avidin and streptavidin against four species of pest Lepidoptera

Two biotin-binding proteins, avidin and streptavidin, were found to be insecticidal to the larvae of four species of Lepidoptera – light brown apple moth, Epiphyas postvittana (Walker) (fam. Tortricidae), green-headed leaf-roller, Planotortrix octo (Dugdale) (fam. Tortricidae), brown-headed leaf-roller, Ctenopseustis obliquana (Walker) (fam. Tortricidae) and potato tuber moth, Phthorimaea operculella (Zeller) (fam. Gelechiidae). Mortality occurred in all species, but there was a wide range in susceptibility. P. operculella larvae were the most susceptible with an LC₅₀ of respectively, 2.3 g ml^–1 for avidin and 1.4 g ml^–1 for streptavidin after 9 days. E. postvittana larvae had an LC₅₀ of 43.4 g ml^–1 for avidin after 21 days, and C. obliquana larvae of 45.7 g ml^–1 for avidin after 28 days. Although significant mortality occurred in P.octo at the highest doses of avidin, there was no sufficient dose-mortality response to calculate an LC₅₀ for this species. For all species mortality curves were steep over a close range of doses followed by a plateau where mortality did not increase significantly with dose and did not reach 100%. Mortality was significantly affected by the amount of biotin in the diet on which the parental generation had been reared. Where this was rich in biotin, significant mortality of the offspring was much lower: larval offspring of a colony of E. postvittana, reared for five generations on a biotin-free diet had an LC₅₀ of 5.1 g ml^–1 after 14 days compared with 76.7 g ml^–1 for larvae from a colony reared on general purpose diet. The implications for use of these proteins to confer insect resistance on transgenic plants are discussed.     

Cadmium interferes with steroid biosynthesis in rat granulosa and luteal cellsin vitro

Recently, cadmium has been described to disturb ovarian function in rats. In this paper the direct influence of cadmium on steroid production of ovarian cellsin vitro has been studied. Granulosa and luteal cells were obtained from proestrous and pregnant rats, and incubated with 0, 5, 10, 20 or 40 g ml^–1 CdCl₂ in the presence or absence of 0.1–1000 ng ml^–1 follicle stimulating hormone (FSH) or luteinizing hormone (LH) for 24 or 48 h. Production of progesterone (P) and 17-estradiol (E₂) by granulosa and that of P by luteal cells were measured by radioimmunoassay. In FSH-stimulated granulosa cell cultures, 5 and 40 g ml^–1 CdCl₂ suppressed P accumulation to 65 and 10%, respectively; accumulation of E₂ (at 5 g ml^–1 CdCl₂) decreased to 44%. P production of LH-supported luteal cells dropped to 86 and 66%, respectively, when 5 and 40 g ml^–1 CdCl₂ was added to the medium. No alteration in basal P accumulation occurred in granulosa and luteal cell cultures following incubations with 20 and 40 g ml^–1 CdCl₂, whereas basal E₂ production of granulosa cells was markedly diminished. It is concluded that CdCl₂ suppressing steroid synthesisin vitro exerts a direct influence on granulosa and luteal cell function.     

Selection of a support for immobilization of a microbial lipase for the hydrolysis of triglycerides

Baterial lipase from Staphylococcus carnosus (pLipMut2) has been immobilized on various supports in order to determine a suitable immobilization technique in terms of activity and stability, when utilized for the hydrolysis of tributyrin. The hydrophobic materials PBA Eupergit and PBA Eupergit 250L prooved to be appropriate supports, when the enzyme was crosslinked with glutaraldehyde after adsorption. No desorption of the immobilized enzyme occured during operation. The pore size of the support has a strong effect on the activity but does not influence stability.The initial activity for immobilized and soluble lipase is found to follow the Arrhenius equation at low temperature, where mass transfer does not affect reaction kinetics. Activation energies for soluble and immobilized lipase were evaluated to be 21.7 kJ mol^–1 and 60.8 kJ mol^–1, respectively.Operational stability was studied in a packed bed recirculation reactor. Thermal desactivation followed first order kinetics with a half-life of 1340 h at 10°C. Model calculations for productivity showed, that optimal temperatures for high productivity are well below the temperature of maximal activity.List of Symbols E _a [kJ mol^–1] activation energy - E _d [kJ mol^–1] activation energy of desactivation - H [–] half-number - k _d [h^–1] desactivation constant - k _d, [h^–1] constant - k _N [–] desactivation constant (number) - N [–] number of runs - p [mol dm^–3] productivity - t [h] time - t _0.5 [h] half-life - T [K] absolute temperature - V [U ml^–1] activity - V(N) [Uml^–1] activity exhibited in the n-th run - V _s,O [U ml^–1] initial activity of supernatant - V _s, [U ml^–1] activity of supernatant after immobilization - V _O [U ml^–1] initial activity - V [U ml^–1] constant - _imm [–] activity yield - [ml ml^–1] ratio of volume of support to volume of supernatant Financial support of this work by the Deutsche Forschungsgemeinschaft (SFB 145, A15) is gratefully acknowledged.     

Feeding rate inhibition in crowded Daphnia pulex

Feeding rates of Daphnia pulex fed a range of levels of the alga Chlamydomonas reinhardi of 15 °C are strongly density-dependent. At lower densities, Daphnia (30 1^–1) fed at higher rates than crowded (270 1^–1) Daphnia which manifest a relatively depressed saturation feeding response. At 30 individuals/liter, Daphnia consumed 8.5 – 15.7 × 10⁴ cells d^–1h^–1 (on a volume basis, 12.1 – 22.2 × 10⁶ m³), at 270 L^–1 3.7 – 3.9 × 10⁴ (5.2 – 5.5 = 10⁶ m³ cells d^–1h^–1 when feeding on algae at 80 000 cells ml^–1 (11.3 × 10⁶ m³ ml^–1). The feeding rate data best fit an Ivlev feeding function. An autoallelopath might be causing the repression. Water preconditioned with crowded Daphnia completely repressed feeding in uncrowded Daphnia after six hours.     

Population growth of some genera of cladocerans (Cladocera) in relation to algal food (Chlorella vulgaris) levels

We studied the patterns of population growth of 7 cladoceran species (Alona rectangula, Ceriodaphnia dubia, Daphnia laevis, Diaphanosoma brachyurum, Moina macrocopa, Scapholeberis kingi and Simocephalus vetulus) using 6 algal densities, viz. 0.05×10⁶, 0.1×10⁶, 0.2×10⁶, 0.4×10⁶, 0.8×10⁶ and 1.6×10⁶ cells ml^–1, of Chlorella vulgaris for 18 – 30 days. In terms of carbon content these algal concentrations corresponded to 0.29, 0.58, 1.16, 2.33, 4.65 and 9.31 g ml^–1, respectively. Cladocerans in the tested range of algal levels responded similarly, in that increasing the food concentrations resulted in higher numerical abundance and population growth rates (r). The peak population densities were (mean±standard error) 71±5; 17.1±0.4, 3.6±0.3, 12.7±1.1, 18.2±2.7, 15.8±1.0 and 10.9±0.02 ind. ml^–1, respectively for A. rectangula, C. dubia, D. laevis, D. brachyurum, M. macrocopa, S. kingi and S. vetulus. In general, the lowest r values were obtained for D. laevis (0.01±0.001) at 0.05×10⁶ cells ml^–1 food level while the highest was 0.283±0.004 for A. rectangula at 1.6×10⁶ cells ml^–1 of Chlorella. When the data of peak population density for each cladoceran species were plotted against the body length, we found an inverse relation, broadly curvilinear in shape. From regression equations between the food level and rate of population increase, we calculated the theoretical food quantity (the threshold level) required to maintain a zero population growth (r = 0) for each cladoceran species, which varied from 0.107 to 0.289 g ml^–1 d^–1 depending on the body size. When we plotted the cladoceran body size against the corresponding threshold food levels, we obtained a normal distribution curve. From this it became evident that for up to 1300 m body size, the threshold food level increased with increasing body size; however, beyond this, the threshold level decreased supporting earlier observations on rotifers and large cladocerans.