Antigen expression from the ribosomal DNA repeat unit of Giardia intestinalis.

The amitochondrial human intestinal parasite Giardia intestinalis is regarded to be the most ancient living example of single-celled eukaryotes and should display primitive features of pre-metazoan gene regulation. Characterization of E. coli clones which express Giardia antigens from plasmid vectors has revealed that an antigen is encoded by the rDNA repeat unit from the strand complementary to that encoding the rRNAs. The open reading frame (ORF) originates in the spacer region between the small (SS) and large (LS) subunit rRNA genes and terminates within the LS rRNA gene. The promoter region of this ORF has characteristics of both RNA polymerase (pol) II and pol III regulatory sequences, suggestive of gene regulation before these different promoter types evolved. The rDNA repeat unit is located on multiple chromosomal sites which are different in each isolate, although the electrophoretic karyotypes appear very stable in Giardia from both human and animal sources.     

Neural network detects errors in the assignment of mRNA splice sites.

The use of databanks in genetic research assumes reliability of the information they contain. Currently, error-detection in the manually or electronically entered data contained in the nucleotide sequence databanks at EMBL, Heidelberg and GenBank at Los Alamos is limited. We have used a subset of sequences from these databanks to train neural networks to recognize pre-mRNA splicing signals in human genes. During the training on 33 human genes from the EMBL databank seven genes appeared to disturb the learning process. Subsequent investigation revealed discrepancies from the original published papers, for three genes. In four genes, we found wrongly assigned splicing frames of introns. We believe this to be a reflection of the fact that splicing frames cannot always be unambiguously assigned on the basis of experimental data. Thus incorrect assignment appear both due to mere typographical misprints as well as erroneous interpretation of experiments. Training on 241 human sequences from GenBank revealed nine new errors. We propose that such errors could be detected by computer algorithms designed to check the consistency of data prior to their incorporation in databanks.     

SAPID tools: microcomputer programs for analysis of multi-unit nerve recordings

A set of programs is described for the digitization and analysisof electrophysiological recordings in which the nerve impulsesfrom several different cells may be present. Although they weredesigned for analysis of data from insect taste sensilla, theymay be applicable to other multi-unit preparations, and areavailable free from the authors. The programs run on standardMS-DOS compatible microcomputers, using a readily availableanalog-to-digital plug-in board. They are ‘modular’,and break the analysis into several stages, each of which maybe applied to many related files of data in a ‘batch’mode. Program design stresses the involvement of the user indecisions as to the effectiveness and accuracy of the analysisas it proceeds, as well as ease and efficiency of use. The programsuse many graphics screens in color, and are controlled by keyboard-or mouse-operated menus; however, they can also be controlledby command-line parameters for standard or repetitive input.     

Prostaglandin biosynthesis by human decidual cells: effects of inflammatory mediators

There is substantial evidence that decidual activation, in association with infection, is linked with the onset of both preterm and term labor. We therefore undertook the present study to evaluate prostaglandin production and its potential regulation by inflammatory mediators in human decidual cells in primary monolayer culture. Upon attaining confluence, the cells were incubated with endotoxin, interleukin 1 alpha (IL1 alpha), interleukin 1 beta (IL1 beta); or tumor necrosis factor (TNF). Production of prostaglandin (PG) E2 and PGF2 alpha was determined using specific radioimmunoassays. Endotoxin and these cytokines all induced significant concentration-dependent increases in PGE2 and PGF2 alpha production. Our results suggest that term human decidual cells are responsive to endotoxin and cytokines and that generation of these substances in the decidua or nearby (eg. in response to infection) will lead to increased prostaglandin production and uterine contractions.     

Novobiocin-resistance sequences from the novobiocin-producing strain Streptomyces niveus

Two distinct DNA sequences expressing novobiocin resistance in Streptomyces lividans were cloned from the novobiocin-producing species Streptomyces niveus. Clone pGL101 (5kb) conferred resistance to 50 micrograms ml-1 novobiocin, whereas clones pGL102 and pGL103, which carry the same 6.5kb insert but in opposite orientations, expressed resistance to 150 micrograms ml-1. The cloned inserts from pGL101 and pGL103 failed to hybridize with each other or with the cloned novobiocin-resistant gyrB sequence from Streptomyces sphaeroides. Both probes hybridized strongly with DNA from the novobiocin-producing species S. niveus and S. sphaeroides but no hybridization (pGL103) or very weak hybridization (pGL101) was detected with DNA from the non-producing species S. lividans, Streptomyces griseus and Streptomyces antibioticus. S. niveus contains at least three novobiocin-resistance determinants with the pGL101 and pGL103 cloned sequences specific for novobiocin-producing strains of Streptomyces.     

Diagnosis of abdominal masses with percutaneous biopsy guided by ultrasound.

OBJECTIVE--To assess the accuracy and safety of percutaneous biopsy of abdominal masses guided by ultrasound. DESIGN--Prospective study. SETTING--Combined gastroenterology service, Scarborough Hospital. PATIENTS--108 Consecutive patients identified as having a discrete mass on diagnostic ultrasound examination of the abdomen. INTERVENTION--A sample of tissue was obtained with an aseptic technique under local anaesthesia: an 18 steel wire gauge needle (Tru-Cut) was mounted in a spring loaded firing device (Biopty gun) that was advanced under simultaneous ultrasound scanning, permitting precise localisation of the target organ. MAIN OUTCOME MEASURE--Results of histological examination of tissue specimens. RESULTS--Biopsy failed in four patients. Adequate histological specimens were obtained in 104 patients with masses in the liver (31), pancreas (37), kidney (10), and adrenal glands (six) and in 20 undiagnosed abdominal and retroperitoneal masses. Follow up was until death or confirmation of the diagnosis. Three complications but no deaths occurred. Malignancy was suspected in 84 patients before biopsy. This was confirmed in 70 patients, in 26 of whom confirmation of dissemination obviated the need for further investigation. In 10 patients biopsy indicated a previously unsuspected primary tumour, and in 12 it showed only a benign lesion. Among 24 patients considered to have benign disease biopsy showed an unsuspected neoplasm in seven. Use of biopsy thus had a major effect on clinical management in 55 patients. Four false negative but no false positive diagnoses resulted from the procedure. CONCLUSION--Percutaneous biopsy of abdominal and retroperitoneal masses under ultrasound guidance is a safe and accurate method of obtaining a histological diagnosis. The results obtained have a considerable effect on clinical management.     

Physical mapping of deletion breakpoints in patients with X-linked ichthyosis: evidence for clustering of distal and proximal breakpoints

Previous studies have shown that approximately 80% of patients with X-linked ichthyosis have a total deletion of the steroid sulphatase (STS) locus which lies in Xp22.3-Xpter. We show by Southern analysis that a common core of sequences are absent in 78.6% of our cases, suggesting that the deletion breakpoints may be highly clustered. To characterize the region in more detail a long-range physical map of over 3 megabases (Mb) surrounding the STS locus was constructed using pulse-field gel electrophoresis. The map enabled the order of sequences tel-SI19-GMGXY3-[STS,GMGXY19]-GMGX9-[dic56 ,SIII2]-cen and the localization of the deletion breakpoints to be established. In ten cases the pulse-field evidence supports the clustering of breakpoints and indicates a deletion size of 2 Mb in most patients. Five CpG islands have been positioned around the STS locus and may be associated with other loci in the region involved in mental retardation and Kallman's syndrome. The map will be instrumental in an attempt to isolate and characterize the deletion breakpoints and to access other genes located in the region.     

Minitron II system for precise control of the plant growth environment

A transparent, cylindrical chamber system was developed to allow measurement of gas-exchange by small crop canopies in the undisturbed plant growth environment. The system is an elaboration of the Minitron system developed previously to compare growth of small plants in different environments within the same general growth area. The Minitron II system described herein accommodates hydroponic culture and separate control of atmospheric composition in individual chambers. Root and shoot environments are compartmented separately to accommodate atmospheres of different flow rate and/or gaseous composition. A series of 0-rings and tension-adjustable springs allow carbon dioxide in the flowing atmosphere to be analyzed without cross-contamination between chamber compartments or from external gas sources. Carbon dioxide has been maintained at set point +/- 9 g m-3 over a range of CO2 concentrations from 382 to 2725 g m-3 and with an atmosphere turnover rate of 136.7 cm3 s-1 by computer-assisted mass flow controllers. Each chamber has dimensions large enough (61 cm internal diameter, 0.151 m3 internal volume) to allow adequate replication of individual plants for statistical purposes (e.g., up to 36 equally-spaced plant holders). No significant variation in growth or photosynthetic rate of leaf lettuce occurred between chambers for a given set of environmental conditions. Gas-exchange rates in different chambers changed to a similar extent as CO2 concentration in the flowing atmosphere or chamber temperature were varied by the same amount. When coupled with appropriate control systems, Minitron II chambers can provide separate controlled environments for multiple small plants with adequate precision and at relatively low cost.     

Copper deficiency depresses rat aortae superoxide dismutase activity and prostacyclin synthesis

Prostaglandin synthesis shows dependence on lipid hydroperoxides and resultant oxygen derived radical formation. In view of the importance of dietary copper in cytosolic copper dependent superoxide dismutase (Cu/Zn SOD) activity and the role of SOD in oxygen radical formation, the influence of dietary copper on prostacylin (PGI2) synthesis and SOD activity in rat aorta was examined. Copper deficient (0.5 micrograms Cu/g diet) rats showed a significant 47% reduction in PGI2 synthesis rates by aortic ring incubations in comparison to copper adequate (6.0 micrograms Cu/g diet) animals. Aortic SOD activity was reduced by 46% in copper deficiency in comparison to copper adequate animals. Marginal dietary copper (1.6 micrograms Cu/g diet) significantly reduced aortic SOD activity by 32% but was without effect on aortic ring incubation PGI2 synthesis. These results indicate that dietary copper deficiency, and the resultant decrease in SOD activity, depresses aortic PGI2 synthesis.     

The determination of the kinetics of polysaccharide thermal degradation using high temperature viscosity measurements

Information about the thermal degradation of the polysaccharides sodium alginate, carrageenan and carboxymethyl cellulose has been obtained from the time dependence of the viscosity at high temperatures measured using a slit viscometer. The viscosity is related to the molecular weight using previously-published relations between the zero shear specific viscosity and the coil overlap parameter in conjunction with the appropriate Mark-Houwink equation. It is found that alginate is much less stable than carboxymethyl cellulose and carrageenan. Activation energies for depolymerisation obtained from Arrhenius plots in the presence of oxygen ranged from 50 kJ/mol for alginate to 105 kJ/mol for κ-carrageenan.