Horseradish peroxidase based bienzyme elctrode for isocitrate

Coimmobilized horseradish peroxidase and D-isocitrate dehydrogenase were fixed to an oxygen electrode to assemble a bienzyme electrode for isocitrate determination. The linear measuring range for isocitrate of the sensor is between 0.1 and 2.0 mmol. I^?1, the coefficient of variation (20 measurements) is 3.6%. 8 samples per hour can be assayed. With one sensor preparation 140 measurements can be carried out.     

Improving ancient DNA read mapping against modern reference genomes

ABSTRACT: BACKGROUND: Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic material from long-dead organisms is still complicated by a number of issues, including post-mortem DNA damage and high levels of environmental contamination. Together with error profiles specific to the type of sequencing platforms used, these specificities could limit our ability to map sequencing reads against modern reference genomes and therefore limit our ability to identify endogenous ancient reads, reducing the efficiency of shotgun sequencing aDNA. RESULTS: In this study, we compare different computational methods for improving the accuracy and sensitivity of aDNA sequence identification, based on shotgun sequencing reads recovered from Pleistocene horse extracts using Illumina GAIIx and Helicos Heliscope platforms. We show that the performance of the Burrows Wheeler Aligner (BWA), that has been developed for mapping of undamaged sequencing reads using platforms with low rates of indel-types of sequencing errors, can be employed at acceptable run-times by modifying default parameters in a platform-specific manner. We also examine if trimming likely damaged positions at read ends can increase the recovery of genuine aDNA fragments and if accurate identification of human contamination can be achieved using a strategy previously suggested based on best hit filtering. We show that combining our different mapping and filtering approaches can increase the number of high-quality endogenous hits recovered by up to 33%. CONCLUSIONS: We have shown that Illumina and Helicos sequences recovered from aDNA extracts could not be aligned to modern reference genomes with the same efficiency unless mapping parameters are optimized for the specific types of errors generated by these platforms and by post-mortem DNA damage. Our findings have important implications for future aDNA research, as we define mapping guidelines that improve our ability to identify genuine aDNA sequences, which in turn could improve the genotyping accuracy of ancient specimens. Our framework provides a significant improvement to the standard procedures used for characterizing ancient genomes, which is challenged by contamination and often low amounts of DNA material.     

Chest-wall deformity after tissue expansion for breast reconstruction

A prospective longitudinal study of chest-wall deformity after tissue expansion for breast reconstruction was performed in 19 women. CT imaging was a sensitive method for detecting occult deformity. Using a semiquantitative scale for measuring deformity, all patients and 94 percent of expanders had some thoracic abnormality after tissue expansion. Rib and chest-wall contour changes were observed under 81 and 68 percent of the expanders, respectively. Routine chest roentgenograms were not a sensitive method for evaluating these deformities. The magnitude of deformity after unilateral expansion was not significantly different from that after bilateral expansion. Linear regression analysis indicated that early periprosthetic capsular contracture was negatively correlated with chest wall deformity. Only one patient experienced a clinically noticeable complication from chest compression--transient postexpansion exertional dyspnea. After removing the expanders and placing permanent implants along with capsulotomy, the mean deformity index decreased by 57 percent after 10.5 months median follow-up, which was highly significant (p less than 0.001). Our findings suggest that chest-wall deformity is a common occurrence after tissue expansion in patients undergoing breast reconstruction and is usually of minor clinical significance.     

2,3-Butanediol production by Enterobacter aerogenes in continuous culture: role of oxygen supply

Summary The influence of oxygen on growth and production of 2,3-butanediol and acetoin by Enterobacter aerogenes was studied in continuous culture. At all dilution rates (D) studied cell mass increased steadily with increasing oxygen uptake rate (OUR), hence the micro-aerobic cultivation was energy-limited. The biomass yield on oxygen increased with D which suggests that cells need more energy for maintenance functions at lower D. At each D an optimal OUR giving highest volumetric productivity for the sum of butanediol and acetoin was found. The optimal OUR increased with D. The occurrence of optimal OURs results from the various effects of O₂ on growth and specific productivity. The latter was found to be a linear function of the specific OUR irrespective of D. At optimal OUR the cells proved to have equal specific OURs and equal specific productivities representing a fixed relationship between fermentative and respiratory metabolism. The product yield based on glucose and corrected for biomass formation was 80%. A product concentration as high as 43 g/l was obtained at D =0.1 h^–1 while the volumetric productivity was the highest at D =0.28 h^–1 (5.6 g/l and hour). The findings further indicate that growth and product generation are obviously non-associated phenomena. Hence, high productivities may be achievable by cell recycling and cell immobilisation systems. Offprint requests to: W.-D. Deckwer     

Non-random intrachromosomal distribution of chromatid aberrations induced by X-rays,alkylating agents and ethanol in Vicia faba

A reconstructed karyotype of Vicia faba with all chromosomes individually distinguishable was treated with triethylene melamine (TEM), cytostasan (CYT) (a new benzimidazol nitrogen mustard), mitomycin C (MI), ethanol (EA) and X-rays. The distribution within chromosomes of induced chromatid abberations was non-random for all agents. The number of segments involved in aberration clustering corresponded to the number of sites representing constitutive heterochromatin, or the regions immediately adjacent to these, as evidenced by the position of Giemsa marker bands. Which of these potential regions of aberration clustering reacted with preferential involvement in aberrations was, in part at least, dependent upon the inducing agent used. It is argued that this may be due to differences in the base composition and/or molecular conformation of heterochromatic regions. Unexpectedly, the distribution pattern of chromatid aberrations induced by mitomycin C was found to be different from those after treatment with the alkylating agents TEM and cytostasan although mitomycin C is assumed to induce aberrations via alkylation. If mitomycin C-induced aberrations are indeed due to alkylation, this indicates that different alkylating agents do not necessarily result in identical patterns of abberation clustering. The other two alkylating agents and ethanol resulted in similar patterns of preferential distribution of abberations. X-Ray induced chromatid aberrations also showed a non-random intrachromosomal distribution, but the clustering was less pronounced than after treatment with the chemical agents.     

In situ hybridization confirms jumping nucleolus organizing regions in Allium

In situ hybridization with a ¹²⁵I-rDNA clone from Vicia faba was performed against Allium cepa and three strains of top onion, which represent hybrids between A. cepa and A. fistulosum. In principle, the labelling patterns correspond to the patterns of the silver-stained nucleolus organizing regions (NORs) in the same species. This strongly supports the inference drawn from the Ag-NOR patterns that NORs can jump between terminal heterochromatin blocks of different Allium chromosomes in the parental species A. cepa as well as in their interspecific hybrids.     

Intracerebral distribution pattern of radioactive morphine and morphine-like drugs after intraventricular and intrathecal injection

Summary The intracerebral distribution patterns of ¹⁴C-morphine, ³H-dihydromorphine, and ³H-fentanyl after intraventricular injection were studied autoradiographically in rats and rabbits. The extent of permeation into the ventricular wall was measured at different times after injection. The hydrophilic morphine and dihydromorphine could be demonstrated within the tissue up to 4 hours. They seemed to be retained within the gray matter and hindered in crossing fiber bundles. On the other hand, the lipophilic fentanyl was quickly removed from the brain but remained relatively longer demonstrable within the white matter. Also, after intrathecal injection of ¹⁴C-morphine a time dependent spread from the injection site was observed. The use of autoradiography in pharmacological experiments as described was found advantageous. Thus, it is possible to correlate directly, the time course of the pharmacological effect and the respective distribution pattern of the drug applied. This may lead to better information about the probable sites of drug action.     

Synergistic interactions between transforming growth factor beta and fibroblast growth factor regulate Schwann cell mitosis

Cultured Schwann cells divide in response to a limited repertoire of mitogens. In addition to cyclic AMP analogs and reagents that raise intracellular cyclic AMP, the only purified mitogens for Schwann cells are transforming growth factor beta (TGFβ), acidic (a) and basic (b) fibroblast growth factor (FGF), and the BB and AB dimers of platelet-derived growth factor (PDGF). Although individually each one of these growth factors is only weakly mitogenic, it is shown here that when TGFβ and bFGF are added to Schwann cell cultures together, they interact to produce a mitogenic response that is much greater than that produced by either growth factor alone. Both the absolute concentration of each protein and the molar ratio of TGFβ to bFGF determines the magnitude of the Schwann cell response.     

A specific internal RNA polymerase recognition site of VSV RNA is involved in the generation of DI particles.

The 3′ terminal sequences of four different DI particle RNAs ranging in size from 10S to 30S have been determined directly using rapid RNA sequencing methods or deduced, in the case of the fourth DI RNA, from the complementary sequence of a small RNA transcribed from this part of the genome (Schubert et al., 1978). One DI particle (DI 011) contains covalently linked genomic and antigenomic RNA. The 5′ end of this RNA is identical to that of VSV RNA, as determined by annealing for at least 1 kb, as well as to the other DI particle RNAs used in this study. The 3′ ends of the other three DI particle RNAs are exact copies of the common 5′ terminal sequence for 48 nucleotides in two cases and 45 nucleotides in the third. Beyond these complementary regions the sequences are different for each DI RNA. The fact that these regions differ in length by only three nucleotides, despite the wide differences in the overall size of the DI particle RNAs, indicates that if these DIs were formed by the copy-back mechanisms similar to those proposed by Leppert, Kort and Kolakofsky (1977) and Huang (1977), a specific recognition site for the RNA polymerase must be involved in copying the 5′ terminus. We determined the 5′ terminal sequence from position 43–48 at the end of the complementary region and found it to be 5′-GGUCUU-3′. This hexamer is also part of other highly conserved terminal RNA polymerase initiation sites (Keene et al., 1978; Keene, Schubert and Lazzarini, 1979) and may be a specific internal RNA polymerase recognition site. We conclude that this sequence is one of the elements involved in the genesis of DI particle chromosomes containing short complementary sequences at their termini. The ability of the polymerase to resume synthesis at or near a specific recognition site is discussed.