Mechanism and base specificity of DNA Breakage in intact cells by neocarzinostatin

When electrophoresed on an agarose gel, the DNA isolated from neocarzinostatin- (NCS-) treated HeLa cells migrates in a ladder of discrete bands indicative of preferential breakage in the linker region of the nucleosomes. The 5'-termini of the drug-induced DNA strand breaks were characterized by reduction of the nucleoside 5'-aldehyde ends to 5'-hydroxyls followed by incorporation of 32P from [gamma-32P]ATP by polynucleotide kinase and treatment of the DNA with hot alkali and alkaline phosphatase prior to the kinase assay to give the total 5'-termini. In DNA isolated from NCS-treated cells, nucleoside aldehyde accounts for 30-45% of the drug-generated 5' ends; the remainder have PO4 termini. By contrast, 5'-terminal nucleoside aldehyde in DNA cut with the drug in vitro exceeds 80% of the total 5' ends. Of the 32P representing nucleoside aldehyde in DNA from NCS-exposed cells, 77% is in TMP; the rest is in AMP much greater than CMP greater than GMP, a distribution in excellent agreement with that obtained for in vitro drug-treated DNA. DNA sequencing experiments, using the 340 base pair alphoid DNA fragment isolated from drug-treated cells, show that the pattern of breakage produced by NCS within a defined sequence of DNA in intact cells is similar to that in the in vitro reaction, with a preferential attack at thymidylate residues, but a much higher concentration of the drug was required to cause comparable breakage in intact cells.(ABSTRACT TRUNCATED AT 250 WORDS)     

Photosynthesis and water relations and the role of anatomy in Umbilicariaceae (lichenes) from Central Spain

Summary The response of net photosynthesis and dark respiration in eight species of Umbilicariaceae (lichenes) to temperature (-5, 0, 5, 10, 15, 20, 25, 30°C) and irradiance (55, 110, 220, 400, 620 mol photons m^-2 s^-1 PAR) was studied. The samples were collected in montane and alpine localities of the Spanish Sistema Central. The species differed widely in their net photosynthetic rates. The optimal temperature for net photosynthesis in alpine species was significantly lower than in montane species. Montane species were more photophytic than alpine ones. Water saturation and water loss rate were dependent on morphology and particularly anatomy of the thallus. The physiological and structural data are useful in the interpretation of the ecology and altitudinal distribution of the Umbilicariaceae. No adaptation could be linked to particularities of the mediterranean climate.     

Anaerobic degradation of papermill sludge in a two-phase digester containing rumen microorganisms and colonized polyurethane foam

Summary The use of reticulated polyurethane foam as a support material for the immobilization of methanogenic associations and its application to the anaerobic treatment of fine particulate solid wastes was investigated. The colonization of polyurethane support particles in a continuous upflow reactor fed on a mixture of acetate, propionate and butyrate, was both rapid and dense. The combination of rumen microorganisms and colonized support particles in a two-phase digester resulted in an efficient anaerobic decomposition of papermill sludge.     

Deoxyribonucleic acid damage by neocarzinostatin chromophore: strand breaks generated by selective oxidation of C-5' of deoxyribose

Among the lesions induced in DNA by neocarzinostatin chromophore are spontaneous and alkali-dependent base release, sugar damage, and single-strand breaks with phosphate (PO4) at their 3' ends and PO4 or nucleoside 5'-aldehyde at the 5' ends. By measuring alkali-dependent thymine release and decomposition of the 5'-terminal thymidine 5'-aldehyde in drug-cut DNA, we show that the kinetics are the same for each process and that the nucleoside aldehyde is the source of about 85% of alkali-dependent thymine release. Reduction of the 5'-aldehyde ends to 5'-hydroxyls followed by incorporation of 32P from [gamma-32P]ATP by polynucleotide kinase permits their selective quantitation. Nucleoside 5'-aldehyde so measured accounts for over 80% of the drug-generated 5' ends; the remainder have PO4 termini. Since these techniques also include the contribution of alkali-labile sites in the measurement of PO4 ends, DNA sequencing was used to measure the ends directly. Using 3'-32P end-labeled DNA restriction fragments as substrates for the drug, it was found that drug attack at a T results in mainly two bands--the stronger one represents oligonucleotide with 5'-terminal nucleoside 5'-aldehyde and may account for over 90% of a particular break. Its structure was verified by its isolation from the sequencing gel, followed by various chemical and enzymatic treatments. In each case, the mobility of the product on the gel was altered in a predictable manner. In addition to spontaneous breaks, neocarzinostatin also causes alkali-labile breaks preferentially at T residues. These sites are heterogeneous in their sensitivity to alkali and are protected by reduction.     

Leaf area index determination in an alder forest: a comparison of three methods

Leaf area index (LAI) of a stand of adult black alder trees(Alnus glutinosa L., Gaertn.) was determined by means of threeindependent methods. (1) The seasonal course of LAI was directlyobtained by counting leaves in situ and adding up their areas,estimated from harvested subsamples of leaves. (2) The seasonalvariation of LAI in the stand was estimated using the Li-CorLAI-2000 PCA in parallel and with this instrument a VegetationArea Index (VAI, projected area of all phyto-elements) was actuallymeasured. (3) Maximum LAI was calculated from leaf litter collectionstaking into account specific leaf area within different layersof the alder crown. Direct LAI estimates (1) and calculationsfrom leaf litter (3) revealed the same figure of maximum LAI(4.8). This LAI was reached in August. The LAI-2000 PCA capturedthe seasonal variation and underestimated, by 11% on average,the LAI obtained directly. Compared with results gained withother broad-leaved tree species the LAI-2000 PCA values foralder were reliable. It is suggested that this is due to thehorizontal homogeneous structure of the main leaf layer. Thisis in the periphery of the crown, where 90% of the light interceptionoccurs. Taking the het-erogeneity into account a satisfactorycompatibility of the three methods applied to the alder standwas achieved. Key words: Alnus glutinosa, leaf area index, in situ counting, LAI-2000 PCA, litter collections     

Productivity and temperature biology of two snowbed bryophytes

Summary Chlorophyll distribution within the carpets, CO₂ gas exchange under controlled conditions, and heat resistance of the snowbed bryophyte Anthelia juratzkana (Limpr.) Trev. were investigated. Also the gas-exchange parameters of the co-occurring Polytrichum sexangulare Floercke were assessed. Only the uppermost 4 mm layer of Anthelia carpets contains sufficient pigments for photosynthesis. At light saturation and optimal temperatures (6–11°C) the maximum rates of CO₂ uptake are 0.7 mg CO₂ g^-1dw h^-1 in Anthelia and 1.5 mg CO₂ g^-1dw h^-1 in Polytrichum. Gas exchange reaches light saturation at about 300 E m^-2s^-1 in both species. At +2°C the light compensation point is reached at ca. 10E m^-2s^-1 and increases significantly with increasing temperature. The lower temperature compensation point is reached at-4°C in Anthelia and does not drop much below-5°C in Polytrichum. Anthelia cannot sustain net photosynthesis beyond 30°C and Polytrichum not beyond 32°C. Nine month storage under dark, cold and wet conditions does not affect the photosynthetic capability of Anthelia. As a response, however, the net photosynthesis rate is depressed due to an increase of the respiration rates. Polytrichum sexangulare did not tolerate the storage so well. The heat resistance limit of Anthelia is low (39°C). There is evidence that the distribution of the two bryophytes within snowbed communities is determined by their capability to make use of low light intensities and their low temperature demand for optimal photosynthetic rates. Being resistant to long lasting cold, wet, and dark conditions, Anthelia is particularly adapted to grow in the border zone along permanent snowpatches. Polytrichum is more productive and is therefore capable of competing successfully at sites which are less extreme and therefore accessible for higher plants.     

The effect of genomic information on optimal contribution selection in livestock breeding programs

Background

Long-term benefits in animal breeding programs require that increases in genetic merit be balanced with the need to maintain diversity (lost due to inbreeding). This can be achieved by using optimal contribution selection. The availability of high-density DNA marker information enables the incorporation of genomic data into optimal contribution selection but this raises the question about how this information affects the balance between genetic merit and diversity.

Methods

The effect of using genomic information in optimal contribution selection was examined based on simulated and real data on dairy bulls. We compared the genetic merit of selected animals at various levels of co-ancestry restrictions when using estimated breeding values based on parent average, genomic or progeny test information. Furthermore, we estimated the proportion of variation in estimated breeding values that is due to within-family differences.

Results

Optimal selection on genomic estimated breeding values increased genetic gain. Genetic merit was further increased using genomic rather than pedigree-based measures of co-ancestry under an inbreeding restriction policy. Using genomic instead of pedigree relationships to restrict inbreeding had a significant effect only when the population consisted of many large full-sib families; with a half-sib family structure, no difference was observed. In real data from dairy bulls, optimal contribution selection based on genomic estimated breeding values allowed for additional improvements in genetic merit at low to moderate inbreeding levels. Genomic estimated breeding values were more accurate and showed more within-family variation than parent average breeding values; for genomic estimated breeding values, 30 to 40% of the variation was due to within-family differences. Finally, there was no difference between constraining inbreeding via pedigree or genomic relationships in the real data.

Conclusions

The use of genomic estimated breeding values increased genetic gain in optimal contribution selection. Genomic estimated breeding values were more accurate and showed more within-family variation, which led to higher genetic gains for the same restriction on inbreeding. Using genomic relationships to restrict inbreeding provided no additional gain, except in the case of very large full-sib families.     

Developmental expression of the murine Prl-1 protein tyrosine phosphatase gene

The expression of the murine Prl-1 protein tyrosine phosphatase gene was examined in normal embryos from E10.5 through E18.5. Prl-1 mRNA was detected in the brain, neural tube, and dorsal root ganglia, and in several non-neuronal tissues, including the skeletal system. Heart and skeletal muscle were consistently negative. At E13.5, Prl-1 was expressed in the condensing prechondrogenic cells of the vertebrae, whereas at E18.5, Prl-1 mRNA was localized to the hypertrophic chondrocytes. The dynamic expression of Prl-1 during cartilage differentiation may suggest a functional role in skeletal development.