Note: Internal diamagnetic flux measurements on ASDEX Upgrade.

Internal diamagnetic flux measurements, with measurement loops and compensation magnetic probes inside the vacuum vessel, are now available on the ASDEX Upgrade tokamak. The measured diamagnetic flux is compared to that predicted by simulations and calculated from equilibrium reconstruction. The diamagnetic flux measured at 2 positions separated toroidally by 180° in the vacuum vessel is compared.

Real-time diamagnetic flux measurements on ASDEX Upgrade.

Real-time diamagnetic flux measurements are now available on ASDEX Upgrade. In contrast to the majority of diamagnetic flux measurements on other tokamaks, no analog summation of signals is necessary for measuring the change in toroidal flux or for removing contributions arising from unwanted coupling to the plasma and poloidal field coil currents. To achieve the highest possible sensitivity, the diamagnetic measurement and compensation coil integrators are triggered shortly before plasma initiation when the toroidal field coil current is close to its maximum. In this way, the integration time can be chosen to measure only the small changes in flux due to the presence of plasma. Two identical plasma discharges with positive and negative magnetic field have shown that the alignment error with respect to the plasma current is negligible. The measured diamagnetic flux is compared to that predicted by TRANSP simulations. The poloidal beta inferred from the diamagnetic flux measurement is compared to the values calculated from magnetic equilibrium reconstruction codes. The diamagnetic flux measurement and TRANSP simulation can be used together to estimate the coupled power in discharges with dominant ion cyclotron resonance heating.

Use of real-time qPCR to quantify members of the unculturable heterotrophic bacterial community in a deep sea marine sponge, Vetulina sp.

In this report, real-time quantitative PCR (TaqMan qPCR) of the small subunit (SSU) 16S-like rRNA molecule, a universal phylogenetic marker, was used to quantify the relative abundance of individual bacterial members of a diverse, yet mostly unculturable, microbial community from a marine sponge. Molecular phylogenetic analyses of bacterial communities derived from Caribbean Lithistid sponges have shown a wide diversity of microbes that included at least six major subdivisions; however, very little overlap was observed between the culturable and unculturable microbial communities. Based on sequence data of three culture-independent Lithistid-derived representative bacteria, we designed probe/primer sets for TaqMan qPCR to quantitatively characterize selected microbial residents in a Lithistid sponge, Vetulina, metagenome. TaqMan assays included specificity testing, DNA limit of detection analysis, and quantification of specific microbial rRNA sequences such as Nitrospira-like microbes and Actinobacteria up to 172 million copies per microgram per Lithistid sponge metagenome. By contrast, qPCR amplification with probes designed for common previously cultured sponge-associated bacteria in the genera Rheinheimera and Marinomonas and a representative of the CFB group resulted in only minimal detection of the Rheiheimera in total DNA extracted from the sponge. These data verify that a large portion of the microbial community within Lithistid sponges may consist of currently unculturable microorganisms.

A novel explosive process is required for the gamma-ray burst GRB 060614.

Over the past decade, our physical understanding of gamma-ray bursts (GRBs) has progressed rapidly, thanks to the discovery and observation of their long-lived afterglow emission. Long-duration (> 2 s) GRBs are associated with the explosive deaths of massive stars ('collapsars', ref. 1), which produce accompanying supernovae; the short-duration (< or = 2 s) GRBs have a different origin, which has been argued to be the merger of two compact objects. Here we report optical observations of GRB 060614 (duration approximately 100 s, ref. 10) that rule out the presence of an associated supernova. This would seem to require a new explosive process: either a massive collapsar that powers a GRB without any associated supernova, or a new type of 'engine', as long-lived as the collapsar but without a massive star. We also show that the properties of the host galaxy (redshift z = 0.125) distinguish it from other long-duration GRB hosts and suggest that an entirely new type of GRB progenitor may be required.

Relativistic ejecta from X-ray flash XRF 060218 and the rate of cosmic explosions.

Over the past decade, long-duration gamma-ray bursts (GRBs)--including the subclass of X-ray flashes (XRFs)--have been revealed to be a rare variety of type Ibc supernova. Although all these events result from the death of massive stars, the electromagnetic luminosities of GRBs and XRFs exceed those of ordinary type Ibc supernovae by many orders of magnitude. The essential physical process that causes a dying star to produce a GRB or XRF, and not just a supernova, is still unknown. Here we report radio and X-ray observations of XRF 060218 (associated with supernova SN 2006aj), the second-nearest GRB identified until now. We show that this event is a hundred times less energetic but ten times more common than cosmological GRBs. Moreover, it is distinguished from ordinary type Ibc supernovae by the presence of 10(48) erg coupled to mildly relativistic ejecta, along with a central engine (an accretion-fed, rapidly rotating compact source) that produces X-rays for weeks after the explosion. This suggests that the production of relativistic ejecta is the key physical distinction between GRBs or XRFs and ordinary supernovae, while the nature of the central engine (black hole or magnetar) may distinguish typical bursts from low-luminosity, spherical events like XRF 060218.

The afterglow of GRB 050709 and the nature of the short-hard gamma-ray bursts.

The final chapter in the long-standing mystery of the gamma-ray bursts (GRBs) centres on the origin of the short-hard class of bursts, which are suspected on theoretical grounds to result from the coalescence of neutron-star or black-hole binary systems. Numerous searches for the afterglows of short-hard bursts have been made, galvanized by the revolution in our understanding of long-duration GRBs that followed the discovery in 1997 of their broadband (X-ray, optical and radio) afterglow emission. Here we present the discovery of the X-ray afterglow of a short-hard burst, GRB 050709, whose accurate position allows us to associate it unambiguously with a star-forming galaxy at redshift z = 0.160, and whose optical lightcurve definitively excludes a supernova association. Together with results from three other recent short-hard bursts, this suggests that short-hard bursts release much less energy than the long-duration GRBs. Models requiring young stellar populations, such as magnetars and collapsars, are ruled out, while coalescing degenerate binaries remain the most promising progenitor candidates.

An asymptotic-giant-branch star in the progenitor system of a type Ia supernova.

Stars that explode as supernovae come in two main classes. A type Ia supernova is recognized by the absence of hydrogen and the presence of elements such as silicon and sulphur in its spectrum; this class of supernova is thought to produce the majority of iron-peak elements in the Universe. They are also used as precise 'standard candles' to measure the distances to galaxies. While there is general agreement that a type Ia supernova is produced by an exploding white dwarf star, no progenitor system has ever been directly observed. Significant effort has gone into searching for circumstellar material to help discriminate between the possible kinds of progenitor systems, but no such material has hitherto been found associated with a type Ia supernova. Here we report the presence of strong hydrogen emission associated with the type Ia supernova SN2002ic, indicating the presence of large amounts of circumstellar material. We infer from this that the progenitor system contained a massive asymptotic-giant-branch star that lost several solar masses of hydrogen-rich gas before the supernova explosion.

May 2001: 32 year old female with dural mass encircling cervical spinal cord.

The May COM. A 32-year-old woman with a history of previous mastoid surgery presented with bilateral extremity weakness and ambulatory instability. MRI revealed a dural-based mass completely encircling the upper cervical spinal cord. Workup was significant for an abnormally elevated c-ANCA, positive at a dilution of 1:128. A portion of the lesion was removed by a posterior surgical approach to decompress the cervical cord. Histologic examination of the dura showed a dense granulomatous infiltrate with vasculitis and giant cells; coupled with the positive c-ANCA, the process was felt to be most consistent with Wegener's granulomatosis. Wegener's granulomatosis infrequently involves the dura or meninges and has not previously been reported to affect dura of the cervical cord. Symptomatic improvement followed surgical decompression and high-dose corticosteroid therapy, with resultant resolution of an elevated c-ANCA titer.

Reaching high poloidal beta at Greenwald density with internal transport barrier close to full noninductive current drive.

In the ASDEX Upgrade tokamak, high poloidal beta up to beta(pol) = 3 at the Greenwald density with H-mode confinement has been reached. Because of the high beta, the plasma current is driven almost fully noninductively, consisting of 51% bootstrap and 43% neutral beam driven current. To reach these conditions the discharge is operated at low plasma current ( I(P) = 400 kA) and high neutral beam heating power ( P(NBI) = 10 MW). The discharge combines an edge (H mode) and internal transport barrier at high densities without confinement-limiting MHD activities. The extrapolation to higher plasma currents may offer a promising way for an advanced scenario based fusion reactor.

Three new peroxides from the sponge Plakinastrella species.

Two new five-membered-ring peroxide acids, plakinic acid F (3) and epiplakinic acid F (4), and a new peroxide-lactone, plakortolide F (5), were isolated from a sponge of the genus Plakinastrella collected from Felicite Island, Seychelles. The structures were elucidated through spectral analysis. The free acids 3 and 4 exhibit moderate antifungal activity against Candida albicans with minimum inhibitory concentrations of 25 micrograms/mL (SDB) and 3.1 micrograms/mL (RPMI) for 3, and 25 micrograms/mL (SDB) and 6.25 micrograms/mL (RPMI) for 4, respectively. Both also showed moderate in vitro inhibition of Aspergillus fumigatus with IC90's of 25 micrograms/mL.

The role of small intestinal bacterial overgrowth, intestinal permeability, endotoxaemia, and tumour necrosis factor alpha in the pathogenesis of non-alcoholic steatohepatitis.

BACKGROUND: Small intestinal bacterial overgrowth may contribute to the development of non-alcoholic steatohepatitis, perhaps by increasing intestinal permeability and promoting the absorption of endotoxin or other enteric bacterial products. AIMS: To investigate the prevalence of small intestinal bacterial overgrowth, increased intestinal permeability, elevated endotoxin, and tumour necrosis factor alpha (TNF-alpha) levels in patients with non-alcoholic steatohepatitis and in control subjects. PATIENTS AND METHODS: Twenty two patients with non-alcoholic steatohepatitis and 23 control subjects were studied. Small intestinal bacterial overgrowth was assessed by a combined (14)C-D-xylose and lactulose breath test. Intestinal permeability was assessed by a dual lactulose-rhamnose sugar test. Serum endotoxin levels were determined using the limulus amoebocyte lysate assay and TNF-alpha levels using an ELISA. RESULTS: Small intestinal bacterial overgrowth was present in 50% of patients with non-alcoholic steatosis and 22% of control subjects (p=0.048). Mean TNF-alpha levels in non-alcoholic steatohepatitis patients and control subjects were 14.2 and 7.5 pg/ml, respectively (p=0.001). Intestinal permeability and serum endotoxin levels were similar in the two groups. CONCLUSIONS: Patients with non-alcoholic steatohepatitis have a higher prevalence of small intestinal bacterial overgrowth, as assessed by the (14)C-D-xylose-lactulose breath test, and higher TNF-alpha levels in comparison with control subjects. This is not accompanied by increased intestinal permeability or elevated endotoxin levels.

Frequency of lipid-lowering drug therapy after coronary and carotid operations for atherosclerosis.

BACKGROUND: Coronary artery bypass grafting (CABG) and carotid endarterectomy (CE) are palliative operations for patients with severe atherosclerosis of the coronary or carotid arteries. Secondary preventive measures after these operations have received little attention. METHODS: We conducted a retrospective observational study to determine the frequency of lipid-lowering drug therapy before and after CABG or CE done in 1997. RESULTS: Of the 204 patients who had CABG, 56 (27%) were receiving lipid-lowering drug therapy before admission, and 71 (37%) of 192 were discharged receiving it. Of the 59 patients who had CE, only 12 (20%) were taking a lipid-lowering drug before admission, and 8 (14%) upon discharge. Of those 59 patients, 23 (39%) had coronary artery disease. CONCLUSION: Secondary prevention after coronary or carotid operations for atherosclerosis has been underemphasized at our institution, prompting the establishment of a postoperative risk reduction program.

Secobatzellines A and B, two new enzyme inhibitors from a deep-water Caribbean sponge of the genus Batzella.

Secobatzelline A (1), a new batzelline natural analogue, and secobatzelline B (2), a likely artifact formed during the isolation procedure, have been isolated from a deep-water marine sponge of the genus Batzella. Secobatzellines A and B inhibited the phosphatase activity of calcineurin, and secobatzelline A inhibited the peptidase activity of CPP32. Both compounds showed in vitro cytotoxicity against P-388 and A-549 cell lines. The isolation and structure elucidation of secobatzellines A (1) and B (2) are described.

Discorhabdin P, a new enzyme inhibitor from a deep-water Caribbean sponge of the genus Batzella.

Discorhabdin P (1), a new discorhabdin analogue, has been isolated from a deep-water marine sponge of the genus Batzella. Discorhabdin P (1) inhibited the phosphatase activity of calcineurin and the peptidase activity of CPP32. It also showed in vitro cytotoxicity against P-388 and A-549 cell lines. The isolation and structure elucidation of discorhabdin P (1) are described.

Emerging applications of the single cell gel electrophoresis (Comet) assay. I. Management of invasive transitional cell human bladder carcinoma. II. Fluorescent in situ hybridization Comets for the identification of damaged and repaired DNA sequences in individual cells.

ABSTRACT I: Management of invasive transitional cell human bladder carcinoma. The two main treatment options for invasive transitional cell bladder carcinoma are radiotherapy or primary cystectomy with urinary diversion or bladder substitution. Approximately 50% of patients fail to respond to radiotherapy and such patients so treated are disadvantaged by the absence of predictive information regarding their radiosensitivity, since the tumour gains additional time for metastatic spread before cystectomy is performed. The SF2 clonogenic assay, which measures the surviving fraction of tumour cells after 2 Gy X-ray irradiation, is regarded as a good measure of radiosensitivity. However, the assay is time consuming and provides results for only approximately 70% of human tumours. In this paper three bladder transitional cell carcinoma cell lines (HT1376, UMUC-3 and RT112) were exposed to X-irradiation (0-10 Gy). We have compared the responses obtained using a clonogenic assay and a more clinically feasible alkaline single cell gel electrophoresis (Comet) assay. A very good inverse correlation was obtained between cell survival (clonogenic assay) and mean tail moment (Comet assay) for the three cell lines, indicating that the Comet assay can be used to predict the radio-responsiveness of individual cell lines. The clinical usefulness of the assay for predicting response to radiotherapy in bladder cancer patients is currently being investigated. ABSTRACT II: Fluorescent in situ hybridization (FISH) Comets for the identification of damaged and repaired DNA sequences in individual cells. In mammalian cells the extent of DNA damage is partly and the rate of DNA repair very considerably dependent on DNA position and transcription. This has been established by biochemical techniques which are labour intensive and require large numbers of cells. The Comet assay for overall DNA damage and repair is relatively simple and allows individual cells to be examined. Here we present a protocol for combination of the Comet assay with fluorescent in situ hybridization (FISH) using a p53 gene probe which allows specific observation of p53 sequences within DNA comets. Chromosome-specific probes can also be used. Optimization of the FISH/Comet protocol to include automation of the analysis is currently underway to facilitate future application of the technique to study selective DNA damage and repair in defined sequences in single mammalian cells.

Evaluation of manual and image analysis quantification of DNA damage in the alkaline comet assay.

The alkaline comet assay or single cell microgel electrophoresis assay is a sensitive method of detecting DNA strand breaks and alkali labile sites in individual cells. The results of this assay can be analysed by different methods. In this study we compared analyses of the same slides by a manual method and by image analysis, post-treatment of clone 707 Friend erythroleukaemia cells with H2O2. The parameters which were found to be particularly useful were comet area and comet length (measured manually) and percentage tail DNA, tail moment, tail length and tail length/head radius (L/H), measured using image analysis. The manual method for comet analysis presented in this paper would appear to provide good and reliable comet data. However, the image analysis comet system described offers an alternative analysis method which avoids the need for photomicrographs and tedious manual analysis. The image analysis parameters: % tail DNA, tail moment, tail length and L/H give good consistent results and for large-scale analysis it will, therefore, conceivably be the method of choice.

Desmoid tumor is a clonal cellular proliferation: PCR amplification of HUMARA for analysis of patterns of X-chromosome inactivation.

Desmoid tumor is a locally aggressive, nonmetastasizing soft tissue tumor. Whether desmoid tumor is a truly neoplastic cellular proliferative process or, alternatively, an unchecked reactive process has been a subject of debate. In order to determine whether desmoid tumor is composed of a clonal cell population as opposed to being a polyclonal reactive process, analysis of patterns of X-chromosome inactivation was performed. Hematoxylin and eosin stained sections of paraffin-embedded, formalin-fixed tissues were microdissected to obtain both lesional and normal control samples, and the genomic DNAs were extracted by proteinase K digestion. Following treatment with methylation sensitive restriction endonuclease (Hha I or Hpa II), the genomic DNAs were amplified by polymerase chain reaction (PCR), using nested primers targeted to a highly polymorphic short tandem repeat (STR) of the human androgen receptor (HUMARA). In eight of 12 cases, PCR amplification of the genomic DNAs was successful, and all eight of the amplified cases were heterozygous in the size of the HUMARA target. The remaining cases could not be studied because of failure to amplify DNA. Following digestion with HhaI or Hpa II, uniform patterns of X-chromosome inactivation were found in all eight desmoid tumors, whereas normal control tissue remained heterozygous. These results confirm a clonal composition of the tumors. The demonstration of clonality in the tumors in all eight informative cases indicates that desmoid tumor is a true neoplastic process, not an unchecked polyclonal reactive process.

Hamacanthins A and B, new antifungal bis indole alkaloids from the deep-water marine sponge, Hamacantha sp.

Hamacanthin A [1] and hamacanthin B [2] are two bioactive dihydropyrazinonediylbis(indole) alkaloids isolated from a new species of deep-water marine sponge, Hamacantha sp. The hamacanthins are growth inhibitors of Candida albicans and Cryptococcus neoformans. Isolation and structure elucidation of 1 and 2 by nmr spectroscopy are described.

Discobahamins A and B, new peptides from the Bahamian deep water marine sponge Discodermia sp.

Discobahamin A [1] and discobahamin B [2] are two bioactive peptides isolated from a new species of the Bahamian deep water marine sponge Discodermia. The discobahamins are inhibitors of the growth of Candida albicans, and the isolation and structure elucidation of 1 and 2 by nmr and chemical methods is described.

Isolation and structure elucidation of 34-sulfatobastadin 13, an inhibitor of the endothelin A receptor, from a marine sponge of the genus Ianthella.

34-Sulfatobastadin 13 [1] was isolated from the sponge Ianthella sp. Its structure was elucidated by nmr techniques and chemical transformation to bastadin 13 [2]. Compound 1 weakly inhibited binding to the endothelin A receptor (ETA), while compound 2 inhibited growth of Bacillus subtilis.