Hydroxamate-activated peroxidases in potato tuber callus. Interaction with the determination of the cytochrome and the alternative pathways

In potato (Solatium tuberosum L. cv. Bintje and Doré) callus a very active hydrox-amate-stimulated NADH-dependent O₂-uptake develops during the growth of the callus, which is caused by a peroxidase. More than 95% of the peroxidase activity is found in the 40000 g supernatant. The total activity may be as high as 1000 times the respiratory acitivity of the callus tissue. At least two fractions, obtained by Sephadex gel filtration, can be distinguished showing this peroxidase activity, one of about 15 kDa and one > 50 kDa. The main properties of both fractions are: a) Hydroxamate at 0.2–0.5 mM gives half-maximal stimulation. Maximal stimulation is observed with 1–3 mM benzhydroxamate (BHAM) and 1–15 mM salicylhydroxamate (SHAM). Higher concentrations, especially of BHAM, give less or no stimulation. b) Hydroxamates are not consumed during the reaction. c) Both NADH and NADPH can serve as the electron donor for the reaction. The affinity for NAD(P)H is very low (K_m near 10 mM). In the absence of hydroxamates NAD(P)H is only slowly oxidized, with an even lower affinity. d) The peroxidase can carry out two reactions: an O₂-consuming and a H₂O₂-consuming reaction. In both reactions one NAD(P)H is consumed. In the first reaction H₂O₂ is formed which can be consumed in the second reaction, resulting in an overall stoichiometry of 2 NADH consumed for each O₂ molecule and in the production of H₂O. e) The reaction is completely blocked by cyanide, superoxide dismutase (EC 1.15.1.1) and (excess) catalase (EC 1.11.1.6), but not by antimycin A or azide. This peroxidase-mediated O₂-uptake might interfere with respiratory measurements. In experiments with isolated mitochondria this interference can be prevented by the addition of catalase to the reaction mixture. The use of high concentrations of hydroxamate is not allowed because of inhibitory effects on the cytochrome pathway. In intact callus tissue hydroxamates only stimulate O₂-uptake in the presence of exogenous NADH. In vivo the peroxidase does not appear to function in O₂-uptake, probably because of its localization (at least partly in the cell wall) and/or its low affinity for NADH. The use of hydroxamates in the determination of cytochrome and alternative pathway activity is discussed.     

Antigenic drift of non-encapsulated Haemophilus influenzae major outer membrane protein P2 in patients with chronic bronchitis is caused by point mutations

The sequence of the gene encoding major outer membrane protein (MOMP) P2 of antigenic variants of non-encapsulated Haemophilus influenzae isolated from persistently infected chronic bronchitis patients was analysed. Antigenic drift was shown to result from single base changes in the P2 gene, all generating amino acid changes in the surface-exposed loops of MOMP P2, predominantly in loop 6. Similar single base changes were observed in H. influenzae persistently present in a subcutaneous cage implanted in rabbits, as well as in a spontaneous H. influenzae mutant that had survived MOMP P2 specific monoclonal-antibody-dependent bactericidal killing in vitro. We hypothesize that accumulation of point mutations under the selection pressure of immunity is a mechanism of antigenic drift of a surface-exposed protein during persistent H. influenzae infection     

Parp1–XRCC1 and the repair of DNA double strand breaks in mouse round spermatids

The repair of DNA double strand breaks (DSBs) in male germ cells is slower and differently regulated compared to that in somatic cells. Round spermatids show DSB repair and are radioresistant to apoptosis induction. Mutation induction studies using ionizing irradiation, indicated a high frequency of chromosome aberrations (CA) in the next generation. Since they are in a G1 comparable stage of the cell cycle, haploid spermatids are expected to repair DSBs by the non-homologous end-joining pathway (NHEJ). However, immunohistochemical evidence indicates that not all components of the classical NHEJ pathway are available since the presence of DNA-PKcs cannot be shown. Here, we demonstrate that round spermatids, as well as most other types of male germ cells express both Parp1 and XRCC1. Therefore, we have determined whether the alternative Parp1/XRCC1 dependent NHEJ pathway is active in these nuclei and also have tested for classical NHEJ activity by a genetic method. To evaluate DSB repair in SCID mice, deficient for DNA-PKcs, and to study the involvement of the Parp1/XRCC1 dependent NHEJ pathway in round spermatids, the loss of γ-H2AX foci after irradiation has been determined in nucleus spreads of round spermatids of SCID mice and in nucleus spreads and histological sections of Parp1-inhibited mice and their respective controls. Results show that around half of the breaks in randomly selected round spermatids are repaired between 1 and 8 h after irradiation. The repair of 16% of the induced DSBs requires DNA-PKcs and 21% Parp1. Foci numbers in the Parp1-inhibited testes tend to be higher in spermatids of all epithelial stages reaching significance in stages I–III which indicates an active Parp1/XRCC1 pathway in round spermatids and a decreased repair capacity in later round spermatid stages. In Parp1-inhibited SCID mice only 14.5% of the breaks were repaired 8 h after irradiation indicating additivity of the two NHEJ pathways in round spermatids.     

3DM: Systematic analysis of heterogeneous superfamily data to discover protein functionalities

Ten years of experience with molecular class–specific information systems (MCSIS) such as with the hand‐curated G protein–coupled receptor database (GPCRDB) or the semiautomatically generated nuclear receptor database has made clear that a wide variety of questions can be answered when protein‐related data from many different origins can be flexibly combined. MCSISes revolve around a multiple sequence alignment (MSA) that includes “all” available sequences from the entire superfamily, and it has been shown at many occasions that the quality of these alignments is the most crucial aspect of the MCSIS approach. We describe here a system called 3DM that can automatically build an entire MCSIS. 3DM bases the MSA on a multiple structure alignment, which implies that the availability of a large number of superfamily members with a known three‐dimensional structure is a requirement for 3DM to succeed well. Thirteen MCSISes were constructed and placed on the Internet for examination. These systems have been instrumental in a large series of research projects related to enzyme activity or the understanding and engineering of specificity, protein stability engineering, DNA‐diagnostics, drug design, and so forth. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Continued decline in tree euphorbias (Euphorbia tetragona and E. triangularis) on the Great Fish River Reserve,Eastern Cape,South Africa

A dramatic decline averaging 43% over a 4‐year period has occurred in tree Euphorbia (Euphorbia tetragona and Euphorbia triangularis) populations on the Great Fish River Reserve, South Africa. These changes are evident from data gathered by general vegetation monitoring methods as well as from a focused study of four tree Euphorbia populations. The decline from 2003 to 2007 was more marked for E. triangularis than for E. tetragona and was accompanied by a general absence of seedlings and a reduced presence of younger age classes of both species, decreasing the proportion of younger trees in the populations. The role of megaherbivores, specifically the black rhinoceros, in these changes is well established. However, the impact of baboon activity, leading to damage to tree crowns and upper branches, is also substantial, especially on E. triangularis populations. Damaged crowns were recorded significantly more often for E. triangularis than for E. tetragona, and the damage frequency increased with decreasing tree height. Thus, our work provides the first evidence that these two closely related Euphorbia species may be affected differently by herbivory.     

Habitat selection by blue swallows Hirundo atrocaerulea Sundevall, 1850 breeding in South Africa and its implications for conservation

This study investigated the utilization of mist‐belt grassland habitat by the threatened blue swallow and was conducted over three successive breeding seasons in the Blue Swallow Natural Heritage Site at Kaapsehoop, Mpumalanga, South Africa. Blue swallows significantly preferred wetlands over grasslands for foraging. Sufficient foraging habitat must be within a 1.5 km radius from an active nest site. The minimum size of a pair of blue swallows home range should be 333 ha, consisting at a minimum of grasslands (243 ha or 73%) and wetlands (90 ha or 27%). In order to conserve this threatened species, habitat transformation should not take place within a minimum radius of 1.5 km of any blue swallow nest. Due to the critical dependence of the blue swallow on wetland habitat for foraging, any development outside the 1.5 km radius that would affect hydrology and water quality within this range would need to be considered, and any adverse effect mitigated. Rehabilitation of areas to a grassland/wetland mosaic would rather quickly support foraging, and eventually breeding. Although a better understanding of the dynamics between wetlands and adjacent grasslands regarding blue swallow habitat requirements is needed, action can already be taken, based on our results.