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Restriction-fragment map of the temperate Bacillus subtilis bacteriophage SPO2.

The endonucleases BglI, BglII, EcoRI, SalI, SmaI, and XbaI were used to fragment the phage SPO2 DNA. Electrophoretic analysis using ethidiumbromide agarose gels showed the phage to have nine BglI sites, one BglII site, four EcoRI sites, one SalI site, one SmaI site, and six XbaI sites. Using partial digestions, multiple endonuclease digestion, and autoradiography the fragments were sized and ordered into a circular map of 23 Md. Such an analysis locates the endonuclease sites, indicates which endonucleases are potentially useful in cloning with SPO2, and allows insertions and/or deletions in the SPO2 DNA to be characterized.

Bacillus subtilis↗

A physical map of the genome of temperate phage phi 3T.

A physical map of the genome of Bacillus subtilis bacteriophage phi 3T was constructed by ordering the fragments produced by cleavage of phi 3T DNA with restriction endonucleases AvaII (2 fragments), BglI (2 fragments), SmaI (3 fragments), BamHI (6 fragments), SalI (7 fragments), AvaI (7 fragments), SacI (12 fragments), PstI (14 fragments), and BglII (26 fragments). Two techniques were used to order the fragments: (1) Sets of previously ordered restriction fragments were isolated and redigested with the endonuclease whose cleavage sites were to be mapped. (2) Fragments located near the ends of the genome or near the ends of other restriction fragments were ordered by treating the DNA with lambda exonuclease prior to restriction endonuclease cleavage. The susceptibility of phi 3T DNA to 15 other restriction endonucleases is also reported.

Bacillus subtilis↗

Restriction mapping of the DNA of the Streptomyces temperate phage phi C31 and its derivatives.

DNA of phi C31 propagated on Streptomyces lividans 66 contained no sites for the restriction enzymes BamHI, SalPI (=PstI) and XhoI; one for XbaI; three for HpaI; five for ClaI and KpnI; six for EcoRI; about 13 for HindIII; about 14 for BclI; and more than 15 for FspAI, HgiAI, SacI, SalGI and SmaI. A complete map of 20 sites (XbaI, HapI, ClaI, KpnI and EcoRI) was obtained using partial digestion and double digestion of DNA of the wild-type and deletion and insertion mutants. The total molecular size was estimated to be 41.2 kb.

Bacteriophages↗

New derivatives of the Streptomyces temperate phage phi C31 useful for the cloning and functional analysis of Streptomyces DNA.

The thiostrepton resistance gene (tsr) of Streptomyces azureus, and a synthetic oligonucleotide adapter sequence, were introduced into the DNA of attP-site-deleted phage phi C31-based cloning vectors. The DNA of two of the new derivatives, KC515 and KC516, contains single sites for the enzymes BamHI, BglII, PstI, PvuII, SstI (two sites close together) and XhoI, available for the insertion of DNA of up to 4 kb. The two vectors also contain a cloned, promoterless viomycin phosphotransferase gene (vph) from Streptomyces vinaceus. When an internal segment of the Streptomyces coelicolor glycerol (gyl) operon was inserted at the appropriate position and in the correct orientation next to vph, it could bring about in vivo recombination leading to fusion of vph of the chromosomally located gyl operon, resulting in glycerol-regulated expression of viomycin resistance. Two other new phi C31 derivatives, KC505 and KC518, are PstI and BamHI replacement vectors, respectively, for 2-8-kb DNA fragments, and allow simple screening for the presence of inserted DNA.

Bacteriophages↗

The primary structure of the operons coding for Shigella dysenteriae toxin and temperate phage H30 shiga-like toxin.

Nucleotide(nt) sequences were determined for the toxin (SHT) operon present in the chromosome of Shigella dysenteriae 1 and for the shiga-like toxin (SLT) operon found in the lambdoid phage H30 genome. The coding sequences of the sht and slt genes differ in 4 nt with 1 nt change responsible for an amino acid replacement. The deduced amino acid sequence in the A chain of the toxins is highly homologous to that of the A chain of ricin, a plant toxin. SHT-coding mRNAs were detected by mapping the 5' termini and using blot-hybridisation; one of them was more abundant and coded only for the B subunit of SHT while the other (bi-cistronic mRNA) encoded both subunits. An IS element related to the IS3 element of Escherichia coli was found in the chromosome of S. dysenteriae near the sht operon.

Amino Acid Sequence↗

Transcriptional analysis of the repressor gene of the temperate Streptomyces phage phi C31.

A 397-bp fragment that contained the 5' end of the coding region of the repressor gene of the temperature Streptomyces phage phi C31 was shown by in vivo promoter-probing to possess bidirectional promoter activity. In vitro runoff transcription experiments, and high resolution transcript mapping of mRNA species produced in vivo using both nuclease S1 and mung bean nuclease, indicated the probable presence of two promoters for the repressor gene with two further promoters oriented in the opposite direction. An inverted repeat sequence is situated 20 bp downstream from the translational stop codon of the repressor gene; high resolution transcript mapping revealed an mRNA endpoint close to this sequence, indicating its likely role as a transcriptional terminator.

Bacteriophages↗

Genetic and sequence analysis of the cos region of the temperate Pseudomonas aeruginosa bacteriophage, D3.

The location and structure of the cos ends of bacteriophage D3, which infects Pseudomonas aeruginosa strain PAO, has been determined using a combination of deletion analysis, transposon mutagenesis, and sequencing directly off the phage DNA. Phage D3 was found to have 9-bp 3' cos ends, making it the first phage of a Gram-negative organism known to have 3' cos ends. A 700-bp region flanking the cos site was necessary for efficient transduction of D3 cosmid derivatives. This region was found to contain incomplete inverted repeat sequences flanking the cos site, along with adenine-rich repeats homologous to coliphage gama Ter binding sites. Possible IHF binding sites were also present.

Base Sequence↗

Temper tantrums.

Explore the source record for details and available documents.

Child Behavior↗

Characterization of a temperate phage hosted by Alcaligenes eutrophus strain A5.

Nineteen strains of Alcaligenes eutrophus were tested for the presence of prophages. One strain that lysed upon mitomycin C treatment produced a phage which could not form plaques on any of the strains available. DNA extracted from partially purified phage lysates was digested with various restriction enzymes which showed that the 42 kb long viral double-stranded DNA circularizes by means of cohesive ends. To our knowledge, this is the first description of a phage for the genus Alcaligenes.

Alcaligenes↗

Reproductive performance of gilts and sows in temperate versus subarctic and arctic zones of Norway.

The reproductive performance of gilts and sows from two regions in Norway was investigated in a retrospective analysis of data from the litter recording system. In the Northern region (North; between 65 degrees N and 71 degrees N), there are extreme shifts in natural photoperiod between winter and summer. In the Southern region (South; between 59 degrees N and 60 degrees 30'N), photoperiodic changes are less dramatic. Gilts were 8 days older at first mating or insemination in the North than in the South (P<0.01). A significantly lower proportion of sows in the North were mated or inseminated within 5 days post-weaning than in the South, a difference present both among primiparous and multiparous sows (P<0.01). Overall farrowing rate in the North was lower than in the South, but litter size (total number born) among those pigs that farrowed was larger. After correction for year, month, breed and age at first service, there were still lower odds of farrowing for gilts in North than in South. Neither for primiparous nor multiparous sows were regional differences in farrowing probability significant when year, month, breed and weaning to service interval were included in the model. Gilts and primiparous sows had a lower probability of farrowing following insemination during summer or autumn months, but service month was not significantly related to the farrowing probability of multiparous sows. For gilts, litter size was positively related to age at first service. For sows, litter size was lowest at weaning to service intervals between 6 and 10 days. Total numbers of piglets born per litter were estimated to be 0.36, 0.38 and 0.55 larger in the North than in the South (differences in least square means; gilts, primiparous sows and multiparous sows, respectively) (P<0.01). Litter size was lower after service during natural long photoperiod than during the rest of the year.

Aging↗

Temporal changes of 7 Be and 210 Pb concentrations in surface air at temperate latitudes 40 degrees N.

Atmospheric concentrations of (7)Be and (210)Pb were measured for 15 years (1987--2001) in ground-level air at Thessaloniki, Northern Greece (40 degrees 38'N, 22 degrees 58'E). Mean activity concentrations of (7)Be and (210)Pb were 5.02 mBqm(-3) and 664 microBqm(-3), respectively, characteristic of the latitude of 40 degrees N. Monthly atmospheric concentrations of (7)Be showed a strong seasonal trend with the highest values being observed in the summer and the lowest in the winter period. Multiple regression analysis of the data of (7)Be concentrations and a number of meteorological parameters revealed that the sunspot number and temperature are the most significant parameters affecting the concentrations of (7)Be in surface air. The observed strong positive correlation between the mean monthly concentrations of (7)Be and the temperature confirms that the increased rate of vertical transport within the troposphere, especially during the warm months, has as a result to carry down to the surface layer air masses enriched in (7)Be. Highest values of the mean monthly atmospheric concentrations of (210)Pb were observed in the autumn and lowest in the spring period. The positive correlation that was observed between (210)Pb and (7)Be concentrations during the summer months suggests that these two radionuclides could be used together as tracers of environmental processes.

Air Pollutants, Radioactive↗

Formation of reactive species and induction of antioxidant defence systems in polar and temperate marine invertebrates and fish.

High oxygen solubility at cold-water temperature is frequently considered to be responsible for an apparently elevated level of antioxidant protection in marine ectotherms from polar environments. However, tissue oxidative stress is in most cases a function of elevated or variable pO2, rather than of an elevated tissue oxygen concentration. This review summarizes current knowledge on pro- and antioxidant processes in marine invertebrates and fish, and relates reactive oxygen species (ROS) formation in polar ectotherms to homeoviscous adaptations of membrane and storage lipids, as well as to tissue hypoxia and re-oxygenation during physiological stress.

Animals↗

Performance of differential GPS collars in temperate mountain forest.

To determine the performance of Global Positioning System (GPS) for habitat studies in free-ranging animals, we tested differential 6- and 8-channel GPS collars under six representative canopies and one open-field reference site in the 'Parc national des Cévennes', southern France. The proportion of successful locations decreased under taller trees and worsened with snow accumulation in mixed coniferous habitats. The mean location success of seven free-ranging red deer fitted with 6-channel GPS collars in the same study area increased with a shorter interval between location attempts and during the leaf-off period. Our data suggested that the differences in location success between leaf-on and leaf-off periods might reflect shifts in habitat use rather than a leaf effect under deciduous trees.

Animals↗

Interannual variability in fish biomarkers in a contaminated temperate urban estuary.

During the past decade the Swan-Canning estuary, Western Australia, has shown signs of stress which has been attributed to high nutrient inputs. There is little information on the effect of nonnutrient contaminants on biota inhabiting the estuary. A suite of biomarkers was measured on black bream (Acanthopagrus butcheri) to determine whether annual variations in fish biomarkers exist in the wet (winter) and dry (summer) seasons. Serum sorbitol dehydrogenase showed no significant differences between years, indicating that measured mixed-function oxygenase (MFO) enzyme activities were not affected by annual variations in hepatic tissue damage. Ethoxyresorufin-O-deethylase activity was lower in female black bream than in male fish while ethoxycoumarin-O-deethylase activity was not influenced by gender. Biomarker levels measured at various sites confirm that major roads and drains are significant contributors of MFO-inducing chemicals into the Swan-Canning estuary. No consistent upstream or downstream gradient in biomarker response was identified. The ratio of naphthalene-type to benzo(a)pyrene-type biliary metabolites was linked to runoff from urban areas into the estuary. There was high annual variability in all biomarkers in both seasons, suggesting that biannual monitoring is required to evaluate the effect of contaminants on the biota in the estuary.

7-Alkoxycoumarin O-Dealkylase↗

Plant senescence: a mechanism for nutrient release in temperate agricultural wetlands.

The beneficial uptake of nutrients by wetland plants is countered to some extent by nutrient release back into the aquatic environment due to vegetative die-back. This current study examined whether Leersia oryzoides, a common wetland plant, exhibits luxury uptake of nutrients from simulated farm runoff. The study also tested whether with subsequent decomposition, these nutrients are released back into the water column. When exposed to elevated (>2mg/L N and P) runoff, L. oryzoides assimilated significantly higher concentrations of nitrogen (p<0.001) and phosphorus (p<0.001) in above-ground biomass as compared to non-enriched treatments (<0.05 mg/L N and P). Subsequently, senescence of enriched above-ground biomass yielded significantly higher concentrations of phosphorus (2.19+/-0.84 mg P/L). Using L. oryzoides as our model, this study demonstrates nitrogen and phosphorus sequestration during the growing season and release of phosphorus in the winter.

Adsorption↗

Gene therapy for immune disorders: good news tempered by bad news.

After a dozen years of human gene therapy trials characterized by minimal gene correction and disappointing clinical impact, the field of gene therapy received some good news in 2000. Infants with X-linked severe combined immunodeficiency who received retroviral gene addition to cells from their bone marrow developed impressive immune reconstitution. During the following 2 years, additional patients were treated and the news was even better-babies receiving gene therapy had sustained T-cell production and in several cases developed better cell function than most patients treated with standard bone marrow transplants. Unfortunately, bad news followed. Three of the patients experienced leukemic T-cell expansions, found to be associated with retroviral insertions into genomic DNA. Where does the field stand today?

Bone Marrow Transplantation↗

Vegetation recovery on closed paths in temperate deciduous forests.

The objective of this study was to evaluate vegetation recovery on footpaths in woodland that have been closed for access for 6 years. A vegetation survey was conducted in four mesophile forests, in transects perpendicular to the trail. Analyses concentrated on the direction and rate of the recovery process. Vegetation on trail sides in these ecosystems recovered substantially. Non-metric multidimensional scaling based upon species composition separated the four sample locations and each cluster contained representatives of the three major trail zones: path centre, transition and undisturbed zones. Analysis of distribution of life forms, plant strategies and seedbank longevity indices showed no differences between trail zones. This indicates that vegetation on the path centre is likely to recover towards the plant composition of the undisturbed zone. Ellenberg values indicate that environmental variation is not related to former path structures, as significant variability was only observed between the forest sites. Furthermore, the analysis concentrated on characteristics of species relevant to the recovery process.

Conservation of Natural Resources↗