Sanger DNA-sequencing reactions performed in a solid-phase nanoreactor directly coupled to capillary gel electrophoresis

A miniaturized, solid-phase nanoreactor was developed to prepare Sanger DNA-sequencing ladders which was directly interfaced to a capillary gel electrophoresis system. A biotinylated fragment of the rat brain actin gene (1 kbp) was amplified by PCR and attached to the interior wall of an (aminoalkyl)silane-derivatized fused-silica capillary tube via a biotin/streptavidin/biotin linkage. Coverage of the capillary wall with the biotinylated DNA averaged 77 +/- 10%. Stability of the anchored template under pressure (33 nL/s) and electroosmotic flows (11.3 nL/s) were favorable, requiring rinsing for > 150 h to reduce the surface coverage by only 50%. In addition, the immobilized template was stable toward temperatures required for preparing sequencing ladders, even under cycling conditions. Standard Sanger dideoxynucleotide termination performed in a large-volume (approximately 8 microL) solid-phase reactor using the thermally stable polymerase enzymes Taq and Vent and the polymerases T7 and Bst with off-line slab gel electrophoresis and autoradiographic detection indicated that acceptable fragment generation was achieved only in the case of the thermally stable polymerases. Banding was not apparent for T7 and Bst since all reagents were inserted into the column in a single plug at the beginning of the reaction. A small volume reactor (volume approximately 62 nL) was then used to perform DNA polymerase reactions and was coupled directly to a capillary gel column for separation. The capillary reactor was placed inside a thermocycler to control the temperature during chain extension and was directly connected to the gel column via zero dead volume fused-silica connectors. The complementary DNA fragments generated (C-track only) in the reactor were denatured using heat and directly injected onto the gel-filled capillary for size separation with detection accomplished using near-IR laser-induced fluorescence. Extension and single-base separation resolution of the C-track, which was directly injected onto the gel column, was estimated to be > 450 bases from the primer annealing site with plate numbers ranging from 1 x 10(6) to 2 x 10(6)/m.     

NMDA receptor-dependent and metabotropic glutamate receptor-dependent forms of long-term depression coexist in CA1 hippocampal pyramidal cells

The development and maturation of the endolymphatic sac (ES) and duct (ED) were studied in the newt Cynops pyrrhogaster. The ES first appears as an oval capsule at the dorsal-medial tip of the otic vesicle at stage 39, about 11 days after oviposition. The ES consists of polymorphous epithelial cells with a minimum of cytoplasm. The intercellular space (IS) between the epithelial cells is narrow and has a smooth surface. At stage 44, the size of the ES increases as many vacuoles in the IS become filled. At stage 46, 18 days after oviposition, the ES elongates markedly and a slit-like lumen is found in the ES. The epithelium contains a few cell organelles which are scattered in the cytoplasm. The vacuoles in the IS are fused, which expands the IS. Two days later (stage 48), floccular material (endolymph) is present in the expanded lumen. The IS dilates and has a wide and irregular appearance. At stage 50, approximately 26 days after oviposition, the ES extends and expands significantly and crystals (otoconia) can now be seen in the widened lumen of the ES. The cytoplasm of the cuboidal epithelial cells contains an abundance of vesicles surrounded by ribosomes and Golgi complexes. Intercellular digitations are formed in the expanded IS. At stage 54, the ES forms a large bellow-like pouch. Numerous otoconia accumulate in the lumen. Free floating cells and cell debris can be seen in the lumen at this stage. The epithelial cells contain numerous cytoplasmic organelles which are evenly distributed in the cytoplasm. Granules are found in the apical and lateral cytoplasm. The IS is loose and displays a labyrinthine appearance. The primitive ED first appears as a connection between the ES and the saccule but no lumen is present inside at stage 39. At stage 46, a narrow lumen is formed in the ED, which corresponds to the formation of the ES lumen. At stage 50, as the ED extends, floccular material is seen in the lumen. At stage 54, the ED bears numerous microvilli on its luminal surface. Otoconia and endolymph are present in the ED. Tight junctions between the epithelial cells are formed at stage 46. A fully developed intercellular junctional complex is produced at stage 54. Based on the development of the ES and ED, the maturation of function of the ES and ED are discussed.     

Studies on the efficacy of hyperbaric rendering procedures in inactivating bovine spongiform encephalopathy (BSE) and scrapie agents

The efficacy of the procedures in use at the two rendering plants in the Netherlands was assessed on a laboratory-scale using procedures that simulated the pressure cooking part of the rendering process. A pool of bovine spongiform encephalopathy (BSE)-infected brainstem from the United Kingdom and a pool of scrapie-infected brainstem from Dutch sheep were used to spike the rendering materials. The mixtures were subjected to various time-temperature combinations of hyperbaric heat treatment related to the conditions used in Dutch rendering plants in the early 1990s, and to the combination of 20 minutes at 133 degrees C required by the EU Directive on rendering of 1996. The efficacy of the procedures in inactivating BSE or scrapie infectivity was measured by titrating the materials before and after heat treatment in inbred mice, by combined intracerebral and intraperitoneal inoculations at limiting dilutions. Two independent series of experiments were carried out. The design of the study allowed for minimum inactivations of up to 2.2 log (2.0 in the second series) to be measured in the diluted infective material and 3.1 log in the undiluted material. After 20 minutes at 133 degrees C there was a reduction of BSE infectivity of about 2.2 log in the first series (with some residual infectivity detected), and in the second series more than 2.0 log (with no residual infectivity detected). With undiluted brain material there was an inactivation of about 3.0 log (with some residual infectivity detected). With the same procedure, scrapie infectivity was reduced by more than 1.7 log in the first series and by more than 2.2 log in the second series. With undiluted brain material there was an inactivation of more than 3.1 log. In each case no residual scrapie infectivity was detected. The BSE agent consistently appeared to be more resistant to heat inactivation procedures than the scrapie agent, particularly at lower temperatures and shorter times.     

Leukoregulin induction of protein expression in human orbital fibroblasts: evidence for anatomical site-restricted cytokine-target cell interactions

The molecular basis for the profound inflammatory response and the accumulation of hyaluronan in orbital connective tissues seen in thyroid-associated ophthalmopathy is unknown. Moreover, the link between the orbital manifestations of Graves' disease and those in the pretibial skin, localized dermopathy, has yet to be established. We have reported recently that leukoregulin, an activated T lymphocyte-derived cytokine, dramatically induces hyaluronan synthesis and prostaglandin-endoperoxide H synthase 2 in human orbital fibroblasts in culture. In the current studies, utilizing giant two-dimensional gel electrophoresis, we find that orbital fibroblasts express constitutively a protein profile that distinguishes them from skin fibroblasts derived from the abdominal wall and from the pretibium. We further demonstrate that leukoregulin, when present in culture medium for 16 hr, up-regulates a set of orbital fibroblast proteins not present in untreated cultures or in fibroblasts from the abdominal wall. However, some of the same protein inductions are present in the pretibial fibroblasts. These leukoregulin-induced changes in protein expression are completely blocked by dexamethasone (10 nM). Our findings are the first to identify proteins that appear to be expressed and differentially regulated in an anatomical site-restricted manner in orbital and pretibial fibroblasts and seem to establish a molecular link between fibroblasts from the orbit and those in pretibial skin.     

Charnley total hip arthroplasty in patients less than fifty years old. A twenty to twenty-five-year follow-up note

We evaluated the results twenty to twenty-five years after ninety-three consecutive, nonselected Charnley total hip arthroplasties performed with cement by the senior one of us in sixty-nine patients who were less than fifty years old at the time of the procedure. Seventy of the seventy-two hips in the living patients were followed radiographically for at least twenty years. Twenty-seven hips (29 per cent) had a revision or a resection of the prosthesis during the follow-up period. The revision or the resection was performed because of aseptic loosening in twenty-one hips (23 per cent), infection in four (4 per cent), dislocation in one (1 per cent), and fracture of the femur in one. Eighteen acetabular components (19 per cent) and five femoral components (5 per cent) were revised because of aseptic loosening, and an additional fourteen acetabular components (15 per cent) and seven femoral components (8 per cent) demonstrated definite or probable radiographic loosening. The present study demonstrates the long-term durability of total hip arthroplasty performed with cement in an active population of patients. The fixation of the femoral component was found to perform better than that of the acetabular component at twenty to twenty-five years after the procedure.     

Increased incidence of spina bifida occulta in fluorosis prone areas

Spina bifida, a congenital deformity of the posterior wall of vertebrae of the spine, is a midline defect of skin, vertebral arches and neural tube, usually in the lumbosacral region. Its incidence is reported to be 0.2 to 0.4 per 1000 live births. Various hypotheses have been put forward as etiological factors for spina bifida including consumption of potato affected by blight and hardness of drinking water but these have not been proven. Two groups of 50 randomly chosen children were established. The study group consisted of children aged 5 to 12 years, weighing 15 to 30 kg, consuming fluoride rich drinking water (4.5 and 8.5 ppm fluoride; WHO permissible limit is 1.5 ppm fluoride), and manifesting either clinical, dental and/or skeletal fluorosis. The control group consisted of age and weight-matched children, consuming less than or equal to 1.5 ppm fluoride in drinking water and not showing any evidence of fluoride toxicity. These children were evaluated for antenatal history, general clinical examination (especially for dimples, tufts of hair, haemangioma on skin throughout the length of spine), other congenital abnormalities, evidence of fluoride toxicity, biochemical estimation for fluoride levels in blood and serum and by skiagrams of the spine to examine for the presence of spina bifida occulta. A total of 22 (44%) of the 50 children in group A, the study group, and 6 (12%) of the 50 children in group B, the control group, revealed spina bifida occulta in the lumbosacral region.(ABSTRACT TRUNCATED AT 250 WORDS)     

Energy consumption modeling and optimization for SRAM's

The recent trends in portable computing technologies have established the need for energy efficient design strategies. To achieve minimum energy design goals, system designers need a technique to accurately model the energy consumption of their design alternatives without performing a full physical design and full-circuit simulation. This paper presents and compares five approaches for modeling the energy consumption of CMOS circuits. These five modeling approaches have been chosen to represent the various levels of model complexity and accuracy found in the current literature. These modeling approaches are applied to the energy consumption of SRAM's to provide examples of their use and to allow for the comparison of their modeling qualities. It was found that a mixed characterization model-using a CV² prediction for digital subsections and fitted simulation results for the analog subsections-is satisfactory (within ±1 process variation) for predicting the absolute energy consumed per cycle. This same model is also very good (within 2%) for predicting an optimum organization for the internal structures of the SRAM. Several common architectures and circuit designs for SRAM's are analyzed with these models. This analysis shows that global, rather than local improvements, produce the largest energy savings     

Regulation of an Escherichia coli/mammalian chimeric carbamoyl-phosphate synthetase

Carbamoyl-phosphate synthetase (CPSase) consists of a 120-kDa synthetase domain (CPS) that makes carbamoyl phosphate from ATP, bicarbonate, and ammonia usually produced by a separate glutaminase domain. CPS is composed of two subdomains, CPS.A and CPS.B. Although CPS.A and CPS.B have specialized functions in intact CPSase, the separately cloned subdomains can catalyze carbamoyl phosphate synthesis. This report describes the construction of a 58-kDa chimeric CPSase composed of Escherichia coli CPS.A catalytic subdomains and the mammalian regulatory subdomain. The catalytic parameters are similar to those of the E. coli enzyme, but the activity is regulated by the mammalian effectors and protein kinase A phosphorylation. The chimera has a single site that binds phosphoribosyl 5'-pyrophosphate (PRPP) with a dissociation constant of 25 microM. The dissociation constant for UTP of 0.23 mM was inferred from its effect on PRPP binding. Thus, the regulatory subdomain is an exchangeable ligand binding module that can control both CPS.A and CPS.B domains, and the pathway for allosteric signal transmission is identical in E. coli and mammalian CPSase. A deletion mutant that truncates the polypeptide within a postulated regulatory sequence is as active as the parent chimera but is insensitive to effectors. PRPP and UTP bind to the mutant, suggesting that the carboxyl half of the subdomain is essential for transmitting the allosteric signal but not for ligand binding.     

Morphologic image processing operators: reduction of partial volume effects for improved 3D visualization of CT data

AIM: The quality of segmentation and three-dimensional reconstruction of anatomical structures in tomographic slices is often impaired by disturbances due to partial volume effects (PVE). The potential for artefact reduction by use of the morphological image processing operators (MO) erosion and dilation is investigated. DESIGN: The CT examinations of 31 patients with pathological alterations in lung or brain were segmented using automatic region growing and the MO were applied in a different number of iterations. The processed regions were 3D-reconstructed (shaded surface display, MIP, volume rendering) and the occurrence of PVE-related artefacts using the signal-to-background ratio (SBR) prior to and after MO application was compared. RESULTS: For all patients under review, the artefacts caused by PVE were significantly reduced by erosion (lung: mean SBRpre = 1.67, SBRpost = 4.83; brain: SBRpre = 1.06, SBRpost = 1.29) even with only a small number of iterations. Region dilation was applied to integrate further structures (e.g. at tumor borders) into a configurable neighbourhood for segmentation and quantitative analysis. CONCLUSIONS: The MO represent an efficient approach for the reduction of PVE artefacts in 3D-CT reconstructions and allow optimized visualization of individual objects.