Measuring stock and change in the GB countryside for policy--key findings and developments from the Countryside Survey 2007 field survey.

Countryside Survey is a unique large scale long-term monitoring programme investigating stock and change of habitats, landscape features, vegetation, soil and freshwaters of Great Britain. Repeat field surveys combine policy and scientific objectives to provide evidence on how multiple aspects of the environment are changing over time, a key goal of international science in the face of profound human impacts on ecosystems. Countryside Survey 2007 (CS2007), the fifth survey since 1978, retained consistency with previous surveys, whilst evolving in line with technological and conceptual advances in the collection and integration of data to understand landscape change. This paper outlines approaches taken in the 2007 survey and its subsequent analysis and presents some of the headline results of the survey and their relevance for national and international policy objectives. Key changes between 1998 and 2007 included: a) significant shifts in agricultural land cover from arable to grassland, accompanied by increases in the area of broadleaved woodland, b) decreases in the length of managed hedges associated with agricultural land, as a proportion deteriorated to lines of trees and c) increases in the areas and numbers of wet habitats (standing open water, ponds) and species preferring wetter conditions (1998-2007 and 1978-2007). Despite international policy directed at maintaining and enhancing biodiversity, there were widespread decreases in species richness in all linear and area habitats, except on arable land, consistent with an increase in competitive and late successional species between 1998 and 2007 and 1978 and 2007. Late successional and competitive species: Stinging nettle (Urtica dioica), Hawthorn (Cratageous monogyna) and Bramble (Rubus fruticosus), in the top ten recorded species recorded in 2007, all increased between 1998 and 2007. The most commonly recorded species in CS (1990, 1998 and 2007) was agricultural Ryegrass (Lolium perenne). Increases in both water quality and soil pH were in line with policy aimed at addressing previous deterioration of both. Headwater streams broadly showed continued improvements in biological quality from 1998 to 2007, continuing trends seen since 1990. In soils, there were significant increases in soil pH between 1998 and 2007 consistent with recovery from acidification.

Resting macrophages produce distinct metabolites from exogenous arachidonic acid.

Resident mouse peritoneal macrophages rapidly metabolize free arachidonic acid (20:4) in the absence of a discernible trigger. After a 20-min incubation in serumless medium, one-third of the fatty acid was found esterified in cell phospholipid and two-thirds was metabolized to oxygenated products which were recovered in the culture medium. The 20:4 oxygenated metabolites were identified by reverse-phase high performance liquid chromatography as hydroxyeicosatetraenoic acids (HETEs) and 6-keto prostaglandin F(1a) (6-ketoPGF(1a)), the stable form of prostacyclin, together with prostaglandin E(2) (PGE(2)) in proportions of 67:24:9. Inhibitor studies using indomethacin, nordihydroguaiaretic acid, and 5,8,11,14-eicosatetraenoic acid confirmed these metabolites to be lipoxygenase and cyclo-oxygenase products. The proportion of products differs considerably from those generated from phospholipid 20:4 in response to a phagocytic stimulus (HETEs:6-ketoPGF(1a):PGE(2):leukotriene C, 15:25:40: 15-20). Cornyebacterium parvum-elicited macrophages incorporated a higher percentage (70 percent) of exogenously supplied 20:4 and converted less than 20 percent of the fatty acid to oxygenated metabolites. Cyclo-oxygenase products (PGE(2), PGF(2a), TXB(2), and 6-ketoPGF(1a)) represented the major 20:4 metabolites (74 percent) synthesized by these activated macrophages. Esterification of 20:4 into cell phospholipids appeared not to be an initial obligatory step for synthesis of 20:4 oxygenated products by this route. To the contrary, incorporation of 20:4 into cell lipids and metabolism via the cyclo-oxygenase and lipoxygenase pathways represent distinct metabolic fates of exogenously supplied 20:4. These observations establish that resting macrophages contain high levels of cyclo-oxygenase and lipoxygenase activity and suggest macrophages can synthesize lipid mediators of inflammation in the absence of an inflammatory stimulus.

Plasma membrane of Entamoeba histolytica.

Axenically propagated Entamoeba histolytica (HK9:NIH strain) were employed as starting material for the isoation of plasma membrane by a novel procedure. In the absence of known enzymatic markers, the externally disposed polypeptides of intact amoebae were iodinated and the incorporated label used to monitor membrane separation and recovery. 12 major plasma membrane polypeptides (12 x 10(3)-200 x 10(3) mol wt) were labeled and separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis. Each of these was a glycoprotein. Preincubation of amoebae with concanavalin A stabilized the plasma membranes as large sheets, facilitating its separation by low-speed centrifugation. Dissociation of the lectin with alpha-methyl mannoside, followed by additional homogenization led to vesiculation and further purification. The isolated plasma membrane was recovered in high yield (28%) and enriched 30-fold in terms of incorporated iodide. All iodinated surface glycoproteins of the intact organism were present in the plasma membrane fraction. A Ca++-dependent ATPase was enriched in the plasma membrane to a similar extent, but over one-half of the total activity was associated with internal, unlabeled membranes, suggesting a dual localization of this activity. The isolated plasma membrane was enriched in cholesterol and had a cholesterol:molar ratio of 0.87. It also contained larger amounts of an unusual phospholipid--ceramide aminoethyl phosphonate--a phospholipase-resistant species.

Endocytosis in Entamoeba histolytica. Evidence for a unique non-acidified compartment.

Our studies on endocytosis in Entamoeba histolytica trophozoites suggest that there are two vacuolar compartments in this organism. The first compartment consists of large vacuoles (greater than 2 microns diameter). As measured by the fluid phase markers, fluorescein isothiocyanate (FITC)-dextran and horseradish peroxidase (HRP), this compartment is a rapid equilibrium with the external milieu and is constantly exchanging (1-2 h) its contents with the external medium. The contents of these vacuoles are not acidified. This together with the absence of degradation of fluid phase markers clearly differentiates these vacuoles from lysosomes of eucaryotes. By labeling externally disposed peptides on the surface membrane of trophozoites with 125I, we could show that the surface membrane was rapidly internalized over a 2-h period and then reached a plateau. All major 125I surface proteins, with the exception of a set of peptides in the 40,000 molecular weight range, were interiorized and approximately 60% of the total radiolabel were found to be in the internal membrane fraction at any given time. The kinetics of this process were similar to those for the uptake of fluid phase markers and are best explained by cycling of the surface membrane into the vacuolar compartment(s) and then back to the cell surface. The second vacuolar compartment consisted of small vesicles (less than 2 microns diameter) with acidified contents as indicated by acridine orange uptake. The endocytic nature of these vesicles was shown by their slow (days) labeling with FITC-dextran, and spectral analysis of internalized FITC-dextran confirmed that this second compartment is acidified (pH 5.2).

Uptake and metabolism of monohydroxy-eicosatetraenoic acids by macrophages.

Within 5 min, resting macrophages metabolize microM quantities of exogenous arachidonic acid (20:4) to cyclooxygenase and lipoxygenase products. Mono-HETEs represent a major class of metabolites recovered from the medium. However, the quantity of mono-Hetes progressively decreases over a 60-min incubation period, with a concomitant increase in more polar lipoxygenase products, suggesting additional metabolic fates for these hydroxy acids. This was directly confirmed by exposing resident macrophage cultures to radiolabeled 15-, 12-, and 5-HETEs (1 microM). 12-30% of the recovered HETEs were cell-associated and predominantly esterified into phospholipid. High pressure liquid chromatography analyses of medium extracts indicated that 50% of each HETE was also converted to 10 or more metabolites over a 60-min time-course, a rate slower than for 20:4. The major metabolite generated from each mono-HETE had the elution characteristics of a di-HETE. The 5-HETE product has a triene spectrum similar to that of 5(S), 12(S)-di-HETE, whereas the 15- and 12-HETE products exhibited single ultraviolet absorption maxima, indicating a metabolic pathway for 5-HETE distinct from the other mono-HETEs. None of the stable cyclooxygenase products of 20:4 (6-keto PGF1 alpha, PGF2 alpha, PGE2, TXB2) nor polar metabolites of mono-HETEs are either incorporated or metabolized. The results indicate that macrophages have the capacity to specifically metabolize 20:4 and mono-HETEs to polar oxygenated products in the absence of a discernible trigger.

Evidence for sequential signals in the induction of the arachidonic acid cascade in macrophages.

We have examined the requirement for Na+, Ca2+, and protein synthesis in the induction of the arachidonic acid (20:4) cascade in cultured murine peritoneal macrophages. Replacement of extracellular Na+ with choline or with K+ inhibited receptor-mediated 20:4 release by 60-90%, but did not inhibit release stimulated by the soluble triggers PMA and A23187. Cells that had preingested zymosan particles in a K+ medium could be induced to secrete 20:4 metabolites merely by changing the medium to one containing Na+. The Ca2+ ionophore A23187 caused cells in Na+-free medium to release and metabolize 20:4 to prostacyclin, PGE2, leukotriene C, and hydroxyeicosatetraenoic acids, suggesting that the phospholipase(s), cyclooxygenase, and lipoxygenase enzymes do not have a requirement for extracellular Na+. These data suggest that receptor-mediated 20:4 secretion has a requirement for extracellular Na+, while 20:4 release triggered by soluble stimuli do not. Immune complex- and A23187-induced 20:4 release was absolutely dependent on extracellular Ca2+. PMA-triggered 20:4 secretion was inhibited 50% in Ca2+-free medium, but could be inhibited completely by preloading the cells with the Ca2+ antagonist quinine. Protein and RNA synthesis was required for 20:4 release induced by zymosan, immune complex, and PMA, but not by A23187. Cycloheximide and emetine were effective within 15 min of addition, while actinomycin D was an effective inhibitor within 45 min. We suggest that receptor-mediated signal response coupling in the 20:4 cascade in macrophages comprises a sequential series of signals that includes an Na+ influx, synthesis of a rapid turnover-protein, and finally an increase in intracellular Ca2+.

Arachidonic acid metabolism by human monocytes. Studies with platelet-depleted cultures.

Purified human monocytes release and metabolize endogenous arachidonic acid (20:4) from phospholipid stores when challenged with particulate inflammatory stimuli or the calcium ionophore A23187. Using radiolabeled cultures, the percentage of total [3H]20:4 released was similar with each type of stimulus. However, the spectrum of 20:4 metabolites differed. With opsonized zymosan (OpZ) or Sephadex beads coated with IgG immune complexes (Ig-beads), the predominant product was thromboxane (25% of the total) together with smaller amounts of other cyclo-oxygenase products and lipoxygenase metabolites. Levels of thromboxane synthesis by monocytes were comparable to those by platelets, as measured by radioimmunoassay. In contrast, exposure to the nonspecific agent A23187 led to mainly lipoxygenase products (70% of the total). Monocytes isolated from mononuclear cell fractions of peripheral blood contain platelets specifically rosetted to their surfaces. These platelet contaminants were removed by sequential incubations of monocytes in serum and EDTA followed by adherence and detachment from tissue culture vessels. The presence of platelets in routinely isolated monocytes presented a major difficulty in the study of human monocyte 20:4 metabolism since platelets also synthesize thromboxane. Loss of 12-HETE synthesis (16-fold reduction relative to 5-HETE) in A23187-stimulated cultures provided a convenient measure of platelet depletion. This together with the response to monocyte-specific stimuli (OpZ and Ig-beads) allowed for the distinction between monocyte and platelet 20:4 metabolism.

Synthesis of leukotriene C and other arachidonic acid metabolites by mouse pulmonary macrophages.

Mouse resident pulmonary macrophages were subdivided into alveolar (PAM) and interstitial (PTM) populations on the basis of accessibility to pulmonary lavage, and zymosan-induced arachidonic acid (20:4) metabolism was examined in both populations labeled with [3H]20:4. Maximal phagocytic doses of unopsonized zymosan induced the specific release of 11% of phospholipid 20:4 by PTM and 4.6% by PAM. Direct fatty acid analysis of [3H]20:4-labeled PTM cultured in the presence or absence of zymosan indicated that the specific activity of the [3H]20:4 in cell phospholipid provided an accurate measure of 20:4 released by the cells, and could therefore be used to quantitate the synthesis of 20:4 metabolites by PTM in vitro. The single major 20:4 metabolite of PTM was the slow-reacting substance leukotriene C, which was synthesized in quantities of 3-4 pmol/microgram cell protein (280-370 pmol/10(6) cells), and comprised 20-25% of the released 20:4. PTM also synthesized prostaglandin E2, prostacyclin, thromboxane A2, and hydroxyeicosatetraenoic acids. In contrast, PAM produced leukotrienes D and E in addition to leukotriene C, prostaglandin E2, thromboxane A2, and hydroxyeicosatetraenoic acids. Prostacyclin formation by PAM was not observed. These studies define a set of experimental conditions for the study of 20:4 metabolism by pulmonary macrophages, and demonstrate that these cells are rich sources of LTC as well as other 20:4 oxygenated products.

Dynamics of leukotriene C production by macrophages.

A method for the radiochemical assay of LTC production by mouse peritoneal macrophages in vitro is presented. The method involves labeling macrophages in culture with [5,6,8,9,11,12,14,15-3H]20:4 followed by stimulation of arachidonic acid (20:4) release under the experimental conditions desired. Radiolabeled leukotriene C (LTC) is recovered from the culture medium by extraction and silicic acid chromatography in 40% yield with full retention of biological activity. Because this LTC is radiochemically pure, the quantity of LTC release may be estimated from the amount of radioactivity in the sample. Use of the radioassay to study parameters affecting LTC synthesis by macrophages indicated that the time course of LTC synthesis and its relationship to the dose of a phagocytic stimulus (zymosan) were very similar to those of prostaglandin (PG) release. LTC release was also similar to that of PG in that lower levels of both metabolites were produced by Corynebacterium parvum-elicited macrophages than by resident cells. Finally, LTC release was stimulated in response to a challenge with antigen-antibody complexes, but lower maximal levels were attained than those with zymosan. The data presented here are consistent with the hypothesis that challenge of macrophages with a phagocytic stimulus leads to the release of 20:4 by an inducible phospholipase. Cyclooxygenase and lipoxygenase then compete for the released 20:4, leading to the production of PG, hydroxyeicosatetraenoic acids, and LTC.

Regulation of arachidonic acid metabolites in macrophages.

The lipids of mouse peritoneal macrophages contain high levels (25 mole percent) of esterified arachidonic acid (20:4). Following in vitro exposure to unopsonized zymosan, these cells synthesize and release oxygenated products of 20:4. Maximal levels of zymosan ingestion promote the release of 40-50% of the 20:4 content of cultures without loss of viabilitiy. Release of radiolabel from macrophages prelabeled with [3H]20:4 provides a quantitative measure for the synthesis of 20:4-derived products. Approximately 67% of the released 20:4 is recovered as prostaglandins (PG) (51% PGE and 16% 6-oxo-PGF1 alpha) and the remainder as apolar products tentatively identified as hydroxy-eicosatetraenoic acids. The kinetics of synthesis are comparable for both sets of products. A detailed examination of PGE synthesis indicated the PGE levels rise in parallel with phagocytosis during a continuous exposure of macrophages to zymosan. The concentration of particles determines the initial rate of PGE release, but the time-course of synthesis is finite (approximately 60 min), regardless of the zymosan dose. These observations are compatible with the notion that phagocytosis results in a burst of PG synthesis, the size of which is determined by the phagocytic stimulus. This is supported by the finding that secondary challenges of zymosan promote new rounds of PG synthesis by macrophages.

Stimulation of human endothelial cell prostacyclin synthesis by select leukotrienes.

Cultured endothelial cells from human umbilical cord labeled with [3H]20:4 release radiolabel when exposed to leukotrienes C or D (LTC or LTD). The major radiolabeled 20:4 metabolite recovered in the culture medium was prostacyclin. Both leukotrienes produced a dose-dependent synthesis of prostacyclin, with a maximal response at 10(-7) M leukotriene. LTC promoted a twofold greater response than did LTD at all concentrations tested (10(-9) to 10(-7) M). In contrast, no release of radiolabel above basal levels was evident with a challenge of LTE or LTB at the same concentrations. Endothelial cells metabolize approximately 40-50% of exogenously supplied LTC to LTD and LTE in 60 min. Levels of alpha-glutamyltranspeptidase (gamma-GTPase), the ectoenzyme reported to convert LTC or LTD, were detected in intact endothelial cells with the chromogenic substrate L-gamma-glutamyl-p-nitroanilide at levels sufficient to account for the observed rate of LTC metabolism. High concentrations of the gamma-GTPase inhibitors, glutathione and AT-125, blocked the metabolism of LTC by endothelium. These results suggest that degradation of leukotrienes by endothelium may be one mechanism for inactivation of these lipid mediators.

Secretion of leukotriene C and other arachidonic acid metabolites by macrophages challenged with immunoglobulin E immune complexes.

Resident mouse peritoneal macrophages release the slow-reacting substance leukotriene C (LTC) on exposure to particulate IgE immune complexes. Because these cells lose their responsiveness to an IgE stimulus after 4 h in culture, maximum release of 20:4 metabolites is observed before this time. However, a similar diminution in 20:4 metabolism was not observed with a zymosan stimulus. Freshly explanted cells are deficient in intracellular glutathione (GSH) (12.4 +/- 0.4 pmol/micrograms cell protein), but GSH increases to a steady state value of 30-35 pmol/micrograms of cell protein between 3 and 9 h of culture. Because GSH is required for the synthesis of LTC and prostaglandin (PG)E2, cultures challenged immediately after explanation have a diminished capacity to synthesize these 20:4 metabolites and release prostacyclin as the major product. By 4-5 h in culture, macrophages form significant amounts of LTC and PGE2. Under optimum conditions of maximum responsiveness to an IgE stimulus and GSH content (after 4 h of culture), macrophages challenged with latex beads coated with IgE immune complexes synthesize 1.0 +/- 0.3 pmol of LTC/microgram cell protein (60 +/- 18 pmol/10(6) cells) in addition to prostacyclin (8.2 +/- 0.8 pmol/micrograms cell protein) and PGE2 (4.7 +/- 1.5 pmol/micrograms cell protein). These amounts are quantitatively similar to the arachidonic acid metabolites produced by macrophages challenged with IgG immune complex-coated latex beads or zymosan. These data demonstrate that macrophages produce large quantities of LTC and other 20:4 metabolites in response to particle-bound IgE and antigen, provided that the appropriate in vitro conditions are met. The macrophage might, therefore, be a major source of slow-reacting substance and other 20:4 metabolites generated during IgE-mediated reactions in vivo.

Regulation of arachidonic acid metabolism by macrophage activation.

Levels of zymosan-induced arachidonic acid (20:4) metabolism by peritoneal macrophages elicited with inflammatory agents and resident macrophages were similar. Thyioglycollate (THIO)-elicited macrophages represented the exception; however, the diminished metabolism by these cells was reproduced by exposing resident cells to 5 mg/ml THIO broth in vitro. In contrast, reduced prostaglandin synthesis by macrophages from mice variously treated with the immunologic agents, Corynebacterium parvum or Bacille Calmette Guérin (BCG), closely correlated with enhanced antitoxoplasma activity, one measure of macrophage activation. This relationship, although not causative, suggested that the capacity for 20:4 metabolism is a function of the macrophage activation state. Modulation of macrophage 20:4 metabolism in vivo apparently required factors in addition to lymphocyte-derived products. Treatment of resident macrophages in vitro with BCG lymphokine was without effect on 20:4 release or prostaglandin synthesis. Activated macrophages from animals inoculated i.p. with C. parvum exhibited reduced 20:4 release and also failed to metabolize 70% of the 20:4 released in response to a zymosan stimulus. Consequently, the quantities of 20:4 metabolites formed were significantly less than expected from 20:4 release. These activated macrophages displayed greatly reduced synthesis of prostacylcin and leukotriene C compared with other 20:4 metabolites. It appeared that factors that regulate macrophage 20:4 metabolism influence the level of the inducible phospholipase and synthetic enzymes for specific 20:4 oxygenated products.

Calcium-binding protein of the chick chorioallantoic membrane. I. Immunohistochemical localization.

The preparation of a specific antiserum (anti-CaBP) against the calcium-binding protein (CaBP) of the chorioallantoic membrane (CAM) is described. The anti-CaBP appeared to be specific for the CaBP by immunodiffusion and immunoelectrophoresis. Application of the anti-CaBP in immunofluorescence histochemistry revealed that the CaBP is present in the CAM only at developmental ages corresponding with the expression of the calcium transport function of the membrane. Furthermore, the CaBP is localized to the ectoderm of the CAM, appears to be exposed to the entire external surface of the ectoderm, and can be shown to be associated with cells enzymatically dissociated from the CAM. These results are consistent with a functional role of the CaBP in the CAM calcium transport process.

Calcium-binding protein of the chick chorioallantoic membrane. II. Vitamin K-dependent expression.

A simple method was devised for the maintenance of the chorioallantoic membrane (CAM) of chick embryos in organ culture. Explants of CAM survived for up to 5 days in this system and retained the characteristic three-layered morphology (ectoderm, mesoderm, and endoderm). Induction of the CAM calcium-binding protein (CaBP) by effectors of calcium metabolism was studied in these organ cultures. Vitamin K was found to elicit a seven- to eightfold increase in CaBP, whereas no increase in CaBP activity occurred on supplementation with vitamin A, parathyroid hormone, an analogue of vitamin D, vitamin D and its hydroxylated metabolites, or with elevated calcium levels. The vitamin K-mediated induction of CaBP was dose-dependent, inhibited by the vitamin K antagonists warfarin and dicoumarol, selective for vitamin K5, and maximal at the developmental stage (13-15 days of incubation) corresponding to the onset of calcium transport by the CAM in vivo. CaBP levels increased after 60-70 h in cultures of 13-15 day CAM supplemented with vitamin K and reached maximal levels around 80-90 h of culture. The CAM ectoderm underwent extensive proliferation and often assumed a villuslike morphology in the vitamin K cultures.

A selective defect in arachidonic acid release from macrophage membranes in high potassium media.

Murine peritoneal macrophages cultured in minimal essential medium (alpha-MEM; 118 mM Na+, 5 mM K+) released arachidonic acid (20:4) from phospholipids on encountering a phagocytic stimulus of unopsonized zymosan. In high concentrations of extracellular K+ (118 mM), 3H release from cells prelabeled with [3H]20:4 was inhibited 80% with minimal reduction (18%) in phagocytosis. The inhibitory effect of K+ on 20:4 release was fully reversed on returning cells to medium containing Na+ (118 mM). Preingestion of zymosan particles by macrophages maintained in high K+ medium resulted in cells being "primed" for 20:4 release, which was only effected (without the further addition of particles) by changing the medium to one containing Na+. In contrast, 20:4 release from cells stimulated with the calcium ionophore A23187 was unimpaired by the elevated K+ medium, suggesting no direct effect of high K+ on the phospholipase. Macrophages stimulated with zymosan in alpha-MEM metabolized the released 20:4 to prostacyclin, prostaglandin E2 (PGE2), and leukotriene C (LTC). The smaller quantity of released 20:4 in high K+ medium was recovered as 6-Keto-PGF1 alpha, the breakdown product of prostacyclin, and PGE2. No LTC was synthesized. In high K+, resting (no zymosan) macrophages synthesized hydroxyeicosatetraenoic acids from exogeneously supplied 20:4 in proportions similar to cells maintained in alpha-MEM. These findings and the similarity of products (including LTC) produced by A23187 stimulated cells in alpha-MEM and high K+ medium indicated that the cyclooxygenase and lipoxygenase pathway enzymes were not directly inhibited by high extracellular K+. We conclude that high concentrations of extracellular K+ uncouple phagocytosis of unopsonized zymosan from the induction of the phospholipase responsible for the 20:4 cascade and suggest that the lesion is at the level of signal transduction between the receptor-ligand complex and the phospholipase.

Derivation of transfer parameters for use within the ERICA Tool and the default concentration ratios for terrestrial biota.

An ability to predict radionuclide activity concentrations in biota is a requirement of any method assessing the exposure of biota to ionising radiation. Within the ERICA Tool fresh weight whole-body activity concentrations in organisms are estimated using concentration ratios (the ratio of the activity concentration in the organism to the activity concentration in an environmental media). This paper describes the methodology used to derive the default terrestrial ecosystem concentration ratio database available within the ERICA Tool and provides details of the provenance of each value for terrestrial reference organisms. As the ERICA Tool considers 13 terrestrial reference organisms and the radioisotopes of 31 elements, a total of 403 concentration ratios were required for terrestrial reference organisms. Of these, 129 could be derived from literature review. The approaches taken for selecting the remaining values are described. These included, for example, assuming values for similar reference organisms and/or biogeochemically similar elements, and various simple modelling approaches.

Chromatin structure of simian virus 40-pBR322 recombinant plasmids in COS-1 cells.

To study the nucleoprotein structure formed by recombinant plasmid DNA in mammalian cells, nuclei were isolated from COS-1 cells after transfection with a recombinant (pJI1) containing pBR322 sequences and a segment of simian virus 40 containing information for a nuclease-sensitive chromatin structure. The nuclei were incubated with DNase I. DNA fragments which were the size of linear pJI1 DNA were isolated, redigested with restriction enzymes, fractionated by electrophoresis, and detected by hybridization with nick-translated segments prepared from the plasmid DNA. Two DNase I-sensitive sites were detected in the simian virus 40 portion of the plasmid at the same sites that were DNase I sensitive in simian virus 40 chromatin prepared late after infection of African green monkey kidney (BSC-1) cells. One site extended from the viral origin of replication to approximately nucleotide 40. The 21-base pair repeated sequences were relatively DNase I resistant. A second site occurred over the single copy of the 72-base pair segment present in this plasmid. These results indicate that the nuclease-sensitive chromatin structure does not depend on the presence of viral structural proteins. In addition, late viral proteins added to pJI1-transfected COS-1 cells by superinfection with simian virus 40 caused no change in the distribution of DNase I-sensitive sites in plasmid chromatin. Analysis of transfected plasmid DNA may provide a general method applicable to the study of the chromatin structure of cloned segments of DNA.

DNA replication and chromatin structure of simian virus 40 insertion mutants.

Insertion of DNA segments into the nuclease-sensitive region of simian virus 40 alters both replication efficiency and chromatin structure. Mutants containing large insertions between the simian virus 40 origin of replication (ori site) and the 21-base-pair repeated sequences replicated poorly when assayed by transfection into COS-1 cells. Replication of mutants with shorter insertions was moderately reduced. This effect was cis-acting and independent of the nucleotide sequence of the insert. The nuclease-sensitive chromatin structure was retained in these mutants, but the pattern of cleavage sites was displaced in the late direction from the ori site. New cleavage sites appeared within the inserted sequences, suggesting that information specifying the nuclease-sensitive chromatin structure is located on the late side of the inserts. Accessibility to BglI (which cleaves within the ori site) was reduced in the larger insertion mutants. These results support the conclusion that efficient function of the viral origin of replication is correlated with its proximity to an altered chromatin structure.

Barriers to nuclease Bal31 digestion across specific sites in simian virus 40 chromatin.

A portion of the nucleoprotein containing viral DNA extracted from cells infected by simian virus (SV40) is preferentially cleaved by endonucleases in a region of the genome encompassing the origin of replication and early and late promoters. To explore this nuclease-sensitive structure, we cleaved SV40 chromatin molecules with restriction enzymes and digested the exposed termini with nuclease Bal31. Digestion proceeded only a short distance in the late direction from the MspI site, but some molecules were degraded 400 to 500 base pairs in the early direction. By comparison, BglI-cleaved chromatin was digested for only a short distance in the early direction, but some molecules were degraded 400 to 450 base pairs in the late direction. These barriers to Bal31 digestion (bracketing the BglI and the MspI sites) define the borders of the same open region in SV40 chromatin that is preferentially digested by DNase I and other endonucleases. In a portion of the SV40 chromatin, Bal31 could not digest through the nuclease-sensitive region and reached barriers after digesting only 50 to 100 base pairs from one end or the other. Chromatin molecules that contain barriers in the BglI to MspI region are physically distinct from molecules that are open in this region as evidenced by partial separation of the two populations on sucrose density gradients.