Structural basis for feedback inhibition of the deoxyribonucleoside salvage pathway: studies of the Drosophila deoxyribonucleoside kinase

Deoxyribonucleoside kinases are feedback inhibited by the final products of the salvage pathway, the deoxyribonucleoside triphosphates. In the present study, the mechanism of feedback inhibition is presented based on the crystal structure of a complex between the fruit fly deoxyribonucleoside kinase and its feedback inhibitor deoxythymidine triphosphate. The inhibitor was found to be bound as a bisubstrate inhibitor with its nucleoside part in the nucleoside binding site and with its phosphate groups partially occupying the phosphate donor site. The overall structure of the enzyme--inhibitor complex is very similar to the enzyme--substrate complexes with deoxythymidine and deoxycytidine, except for a conformational change within a region otherwise directly involved in catalysis. This conformational change involves a magnesium ion, which is coordinated in the inhibitor complex to the phosphates and to the primary base, Glu52, that normally is positioned close to the 5'-OH of the substrate deoxyribose.     

Comparative genomics reveals novel biochemical pathways

How well do we understand which enzymes are involved in the primary metabolism of the cell? A recent study using comparative genomics and postgenomics approaches revealed a novel pathway in the most studied organism, Escherichia coli. The analysis of a new operon consisting of seven previously uncharacterized genes thought to be involved in the degradation of nucleic acid precursors shows the impact of comparative genomics on the discovery of novel pathways and enzymes.     

Microcosm evaluation of bioaugmentation after field-scale thermal treatment of a TCE-contaminated aquifer

This paper investigates effects of combining thermal and biological remediation, based on laboratory studies of trichloroethene (TCE) degradation. Aquifer material was collected 6 months after terminating a full-scale Electrical Resistance Heating (ERH), when the site had cooled from approximately 100°C to 40°C. The aquifer material was used to construct bioaugmented microcosms amended with the mixed anaerobic dechlorinating culture, KB-1^TM, and an electron donor (5 mM lactate). Microcosms were bioaugmented during cooling at 40, 30, 20, and 10°C, as temperatures continually decreased during laboratory incubation. Redox conditions were generally methanogenic, and electron donors were present to support dechlorination. For microcosms bioaugmented at 10°C and 20°C, dechlorination stalled at cis-dichloroethene (cDCE) and vinyl chloride (VC) 150 days after bioaugmentation. However, within 300 days of incubation ethene was produced in the majority of these microcosms. In contrast, dechlorination was rapid and complete in microcosms bioaugmented at 30°C. Microcosms bioaugmented at 40°C also showed rapid dechlorination, but stalled at cDCE with partial VC and ethene production, even after 150 days of incubation when the temperature had decreased to 10°C. These results suggest that sequential bioremediation of TCE is possible in field-scale thermal treatments after donor addition and bioaugmentation and that the optimal bioaugmentation temperature is approximately 30°C. When biological and thermal remediations are to be applied at the same location, three bioremediation approaches could be considered: (a) treating TCE in perimeter areas outside the source zone at temperatures of approximately 30°C; (b) polishing TCE concentrations in the original source zone during cooling from approximately 30°C to ambient groundwater temperatures; and (c) using bioremediation in downgradient areas taking advantages of the higher temperature and potential release of organic matter.     

Evidence from dithizone and selenium zinc histochemistry that perivascular mossy fiber boutons stain preferentially “in vivo”

Summary This paper describes a perivascular staining pattern that is obtained when dithizone or sodium selenite are used to label zinc intravitally. Our observations indicate that the perivascular staining is a result of zinc labeling in mossy fiber boutons adjacent to capillaries and suggest that there might be a special blood brain barrier in the mossy fiber regions.     

Optical slicing and 3-D characterization of hippocampal capillaries in the rat visualized by autometallographic silver enhancement of colloidal gold particles

Summary In order to visualize the vascular system of the rat brain, 10 Wistar rats were perfused transcardially with glutaraldehyde and a 40°C gold-gelatine solution. The brains were post-fixed with glutaraldehyde and vibratomized into 100-μm-thick slices, and the gold particles were developed by autometallography. In this way, the colloidal gold particles in the vessels became encased in silver and thereby made visible. The developed gold staining is stable and does not interfere with further dehydration and counterstaining. Images were frame grabbed during optical slicing, and classic stereograms and ‘shadow’ 3-D images were produced. We found a high variation of capillary density in the hippocampal region reflecting known subregional structures. The silver-enhanced vessels acted as natural markers and made it possible to study and measure aspects of the complexity of dehydration and staining artifacts. We found a non-linear shrinking of 13–17% in the x- and y-directions and a spatial shrinking up to 50% in some regions after the dehydration and staining process. This observation may be of interest not only in relation to tissue subjected to this fixation protocol but also to other fixation procedures. The gold-gelatine autometallographic technique and the present stereograms can release data for stereological use as well This revised version was published online in November 2006 with corrections to the Cover Date.     

Light and electron microscopic localization of silver in biological tissue

Summary A method is described that visualizes trace amounts of silver in frozen, paraffin and epon sections from biological tissue. After exposure to light, which ensures reduction of silver ions that are not bound to sulphide, histological sections from animals treated with silver compounds are exposed to a photographic developer containing silver ions. Tissue silver acts as a catalyst for the hydroquinone reduction of silver ions to metallic silver which then accumulates at the site of the trace deposit. Light and electron micrographs showing silver in different organs from albino rats treated with silver lactate are presented. Localization of silver in motor neurons of the spinal gray matter and pons indicates a transport of silver over the blood-brain barrier. Silver precipitates in fetal liver suggest that silver ions can penetrate the placental barrier.     

Histochemical demonstration of zinc ions in human epididymis using autometallography

Summary A recently described autometallographic technique, allowing demonstration of chelatable zinc in human biopsy material, was applied to cryostat sections from biopsies of human epididymis. Sections from the rat epididymis were used as control materials to examine the quality of the method compared with a previously used autometallographic method. The human epididymis exhibits heavy staining in the head of the epididymis and only small amounts of zinc in the body and tail of the organ. The zinc staining was found in the apical part of the ciliated cells and in the lumen. The present technique can be used to localize zinc ions at ultrastructural levels. Zinc grains were localized in lysosome-like bodies and secretory granules of the ciliated cells. The luminal staining was present as free, evenly dispersed zinc grains or attached to sperm cells and stereocilia in the lumen. The large differences in staining patterns along the epididymal tract in humans and rats suggest that zinc ions are important for the maturation of sperm cells This revised version was published online in November 2006 with corrections to the Cover Date.     

Exogenous selenium in the brain

Summary Transcardial perfusion or intraperitoneal injections with sodium selenite result in the creation of selenium bonds that can be visualized by physical development. The present paper describes how these catalytic bonds are made visible in the tissues by surrounding them with shells of metallic silver. Based on experiments with chelating agents, the possibility that selenium-metal bonds are the catalysts is discussed. In the brain, the selenium pattern is delicate and highly laminated, the grains of silver being orderly arranged corresponding with the neuropil morphology. The precipitate is most densely packed in cortical regions. The difference in staining intensity seen in different regions of the CNS reflects the density of selenium reactive terminals. The visualized selenium bonds are predominantly located within boutons, and examination in the electron microscope reveals accumulation in the presynaptic regions. In a few places precipitates can also be found in axons, but have not been observed in perikarya or dendrites. The only non-neuronal locations of selenium were sparsely scattered, astrocyte-like neuroglia, predominantly found in the cerebellum and the hypothalamus; infrequently a few blood vessels were also stained. Sections from kidney and liver are presented as examples of localizations outside the CNS of exogenous selenium.     

Differential induction of functional IgG using the Plasmodium falciparum placental malaria vaccine candidate VAR2CSA

Background

In Plasmodium falciparum malaria endemic areas placental malaria (PM) is an important complication of malaria. The recurrence of malaria in primigravidae women irrespective of acquired protection during childhood is caused by the interaction between the parasite-expressed VAR2CSA antigen and chondroitin sulfate A (CSA) in the placental intervillous space and lack of protective antibodies. PM impairs fetal development mainly by excessive inflammation processes. After infections during pregnancy women acquire immunity to PM conferred by antibodies against VAR2CSA. Ideally, a vaccine against PM will induce antibody-mediated immune responses that block the adhesion of infected erythrocytes (IE) in the placenta.

Principal Findings

We have previously shown that antibodies raised in rat against individual domains of VAR2CSA can block IE binding to CSA. In this study we have immunized mice, rats and rabbits with each individual domain and the full-length protein corresponding to the FCR3 VAR2CSA variant. We found there is an inherently higher immunogenicity of C-terminal domains compared to N-terminally located domains. This was irrespective of whether antibodies were induced against single domains or the full-length protein. Species-specific antibody responses were also found, these were mainly directed against single domains and not the full-length VAR2CSA protein.

Conclusions/Significance

Binding inhibitory antibodies appeared to be against conformational B-cell epitopes. Non-binding inhibitory antibodies reacted highly against the C-terminal end of the VAR2CSA molecule especially the highly polymorphic DBL6ε domain. Differential species-specific induction of antibody responses may allow for more direct analysis of functional versus non-functional B-cell epitopes.     

Increasing the analytical sensitivity by oligonucleotides modified with para- and ortho-twisted intercalating nucleic acids--TINA

The sensitivity and specificity of clinical diagnostic assays using DNA hybridization techniques are limited by the dissociation of double-stranded DNA (dsDNA) antiparallel duplex helices. This situation can be improved by addition of DNA stabilizing molecules such as nucleic acid intercalators. Here, we report the synthesis of a novel ortho-Twisted Intercalating Nucleic Acid (TINA) amidite utilizing the phosphoramidite approach, and examine the stabilizing effect of ortho- and para-TINA molecules in antiparallel DNA duplex formation. In a thermal stability assay, ortho- and para-TINA molecules increased the melting point (Tm) of Watson-Crick based antiparallel DNA duplexes. The increase in Tm was greatest when the intercalators were placed at the 5' and 3' termini (preferable) or, if placed internally, for each half or whole helix turn. Terminally positioned TINA molecules improved analytical sensitivity in a DNA hybridization capture assay targeting the Escherichia coli rrs gene. The corresponding sequence from the Pseudomonas aeruginosa rrs gene was used as cross-reactivity control. At 150 mM ionic strength, analytical sensitivity was improved 27-fold by addition of ortho-TINA molecules and 7-fold by addition of para-TINA molecules (versus the unmodified DNA oligonucleotide), with a 4-fold increase retained at 1 M ionic strength. Both intercalators sustained the discrimination of mismatches in the dsDNA (indicated by ΔTm), unless placed directly adjacent to the mismatch--in which case they partly concealed ΔTm (most pronounced for para-TINA molecules). We anticipate that the presented rules for placement of TINA molecules will be broadly applicable in hybridization capture assays and target amplification systems.