Role of DNA flexibility in sequence-dependent activity of uracil DNA glycosylase

Uracil DNA glycosylase (UDG) is a base excision repair enzyme that specifically recognizes and removes uracil from double- or single-stranded DNA. The efficiency of the enzyme depends on the DNA sequence surrounding the uracil. Crystal structures of UDG in complex with DNA reveal that the DNA is severely bent and distorted in the region of the uracil. This suggests that the sequence-dependent efficiency of the enzyme may be related to the energetic cost of DNA distortion in the process of specific damage recognition. To test this hypothesis, molecular dynamics simulations were performed on two sequences representing extreme cases of UDG efficiency, AUA/TAT (high efficiency) and GUG/CAC (low efficiency). Analysis of the simulations shows that the effective bending force constants are lower for the AUA/TAT sequence, indicating that this sequence is more flexible than the GUG/CAC sequence. Fluorescence lifetimes of the adenine analogue 2-aminopurine (2AP), replacing adenine opposite the uracil, are shorter in the context of the AUA/TAT sequence, indicating more dynamic base-base interaction and greater local flexibility than in the GUG/CAC sequence. Furthermore, the K(M) of Escherichia coli UDG for the AUA/TAT sequence is 10-fold smaller than that for the GUG/CAC sequence, while the k(cat) is only 2-fold smaller. This indicates that differences in UDG efficiency largely arise from differences in binding and not catalysis. These results link directly flexibility near the damaged DNA site with the efficiency of DNA repair.     

Attitudinal reciprocity in food sharing among brown capuchin monkeys

Capuchin monkeys (Cebus apella) share food even if separated by a mesh restraint. Pairs of capuchins were moved into a test chamber in which one of them received apple pieces for 20 min, and the other received carrot pieces for the next 20 min. Previous research had shown a correlation between the rate of food transfer in both directions across female-female dyads. The present study confirmed this result. Reciprocity across dyads can be explained, however, by symmetry in affiliative and tolerant tendencies between two individuals, provided these tendencies determine food sharing. The present study was designed to exclude this symmetry-based explanation by testing each pair (N=16) of adult females on six separate occasions. There existed a significant covariation across tests of sharing in both dyadic directions, a result unexplained by relationship symmetry. Moreover, control procedures (i.e. testing of a food possessor without a partner, or testing of two individuals with the same food or two different foods at the same time) indicated that behaviour during food trials is not fully explained by mutual attraction or aversion. The monkeys take the quality of their own and the partner's food into account, and possessors limit transfers of high-quality foods. Instead of a symmetry-based reciprocity explanation, a mediating role of memory is suggested, and a mirroring of social attitude between partners. Copyright 2000 The Association for the Study of Animal Behaviour.     

Catalytic generation of N2O3 by the concerted nitrite reductase and anhydrase activity of hemoglobin

Nitrite reacts with deoxyhemoglobin to form nitric oxide (NO) and methemoglobin. Though this reaction is experimentally associated with NO generation and vasodilation, kinetic analysis suggests that NO should not be able to escape inactivation in the erythrocyte. We have discovered that products of the nitrite-hemoglobin reaction generate dinitrogen trioxide (N2O3) via a novel reaction of NO and nitrite-bound methemoglobin. The oxygen-bound form of nitrite-methemoglobin shows a degree of ferrous nitrogen dioxide (Fe(II)-NO2*) character, so it may rapidly react with NO to form N2O3. N2O3 partitions in lipid, homolyzes to NO and readily nitrosates thiols, all of which are common pathways for NO escape from the erythrocyte. These results reveal a fundamental heme globin- and nitrite-catalyzed chemical reaction pathway to N2O3, NO and S-nitrosothiol that could form the basis of in vivo nitrite-dependent signaling. Because the reaction redox-cycles (that is, regenerates ferrous heme) and the nitrite-methemoglobin intermediate is not observable by electron paramagnetic resonance spectroscopy, this reaction has been 'invisible' to experimentalists over the last 100 years.     

The improvement of in vitro cytotoxicity testing for the assessment of acute toxicity in fish

The use of fish cell line cytotoxicity tests as alternatives to acute lethality tests with fish is hampered by the clearly lower sensitivity of the fish cell line tests. Recently, it has been shown that this is not a unique feature of fish cells. In fact, the sensitivity of mammalian and human cell lines toward the cytotoxic actions of chemicals, in general, is comparable to that of fish cell lines. Reviewing some of our recent investigations, the objective of this paper is to show that the sensitivity of in vitro cytotoxicity testing and the correspondence between in vitro cytotoxic and acute fish toxic concentrations (LC50) can be increased, if: a) inhibition of cell growth instead of cell death is used as the endpoint; and b) the bioavailable free cytotoxic concentration (ECu50) of chemicals in vitro, instead of the nominal cytotoxic concentration (EC50), is used as the measure of cytotoxic potency. Based on these results, a pragmatic in vitro testing strategy for estimating the minimal aquatic toxic potency of chemicals is proposed.     

Substrate specificities of the chloromuconate cycloisomerases from Pseudomonas sp. B13, Ralstonia eutropha JMP134 and Pseudomonas sp. P51

The chloromuconate cycloisomerase of Pseudomonas sp. B13 was purified from 3-chlorobenzoate-grown wild-type cells while the chloromuconate cycloisomerases of Ralstonia eutropha JMP134 (pJP4) and Pseudomonas sp. P51 (pP51) were purified from Escherichia coli strains expressing the corresponding gene. Kinetic studies were performed with various chloro-, fluoro-, and methylsubstituted cis,cis-muconates. 2,4-Dichloro-cis,cis-muconate proved to be the best substrate for all three chloromuconate cycloisomerases. Of the three enzymes, TfdD of Ralstonia eutropha JMP134 (pJP4) was most specific, since its specificity constant for 2,4-dichloro-cis,cis-muconate was the highest, while the constants for cis,cis-muconate, 2-chloro- and 2,5-dichloro-cis,cis-muconate were especially poor. The sequence of ClcB of the 3-chlorobenzoate-utilizing strain Pseudomonas sp. B13 was determined and turned out to be identical to that of the corresponding enzyme of pAC27 (though slightly different from the published sequences). Corresponding to 2-chloro-cis,cis-muconate being a major metabolite of 3-chlorobenzoate degradation, the k _cat/K _m with 2-chloro-cis,cis-muconate was relatively high, while that with the still preferred substrate 2,4-dichloro-cis,cis-muconate was relatively low. This enzyme was thus the least specific and the least active among the three compared enzymes. TcbD of Pseudomonas sp. P51 (pP51) took an intermediate position with respect to both the degree of specificity and the activity with the preferred substrate. Received: 7 August 1998 / Received revision: 24 November 1998 / Accepted: 29 November 1998     

The effect of nutrient enrichment on the plankton community in enclosed water columns

Low level nutrient enrichment of an enclosed water column caused increases in primary, secondary and tertiary production. In addition, increases in the amount of sediment material, heterotrophic activity and accumulation of major nutrients, nitrate and phosphate, were noted. In contrast, no change was observed in species diversity that could be attributed to nutrient enrichment. The combination of these effects is suggested as a diagnostic approach to examining the early effects of marine eutrophication.     

Picosecond spectroscopy of the isolated reaction centers from the photosystems of oxygenic photosynthesis—ten years (1987–1997) of fun A tribute to Michael R. Wasielewski on his 60th birthday

Mike Wasielewski’s pioneering work on Photosystem II photochemistry has an important place in the history of photosynthesis; we are proud to have been associated with him in making those first measurements. Here, we present our association and publications with him, and provide some of the history behind this research.     

Voltage-gated sodium channel toxins

Neurotoxins have served as invaluable agents for identification, purification, and functional characterization of voltage-gated ion channels. Multiple classes of these toxins, which target voltage-gated Na⁺ channels via high-affinity binding to distinct but allosterically coupled sites, have been identified. The toxins are chemically diverse, including guanidinium heterocycles, a variety of structurally unrelated alkaloids, and multiple families of nonhomologous polypeptides having either related or distinct functions. This review describes the biochemistry and pharmacology of these agents, and summarizes the structure-function relationships underlying their interaction with molecular targets. In addition, we explore recent advances in the use of these toxins as molecular scaffolding agents, drugs, and insecticides.     

Effects of galactoflavin-induced riboflavin deficiency upon rat hepatic cell ultrastructure.

The primary cytoplasmic effect of galactoflavin-induced riboflavin deficiency upon rat liver cells involved focal sites of degradation which were manifested by the formation of membranous whorls. The nuclear effect of riboflavin deficiency concerned fluctuations in the total number of perichromatin granules per nucleus. These granules increased in number during the deficiency reaching a peak at three weeks. Nucleoli appeared compact with no evidence for segregation of nucleolar components. The possible correlation between increased synthesis of perichromatin granules and altered protein synthesis is discussed.