Chemical and kinetic reaction mechanisms of quinohemoprotein amine dehydrogenase from Paracoccus denitrificans

Quinohemoprotein amine dehydrogenase (QHNDH) possesses a cysteine tryptophylquinone (CTQ) prosthetic group that catalyzes the oxidative deamination of primary amines. In addition to CTQ, two heme c cofactors are present in QHNDH that mediate the transfer of the substrate-derived electrons from CTQ to an external electron acceptor. Steady-state kinetic assays yielded relatively small k(cat) values (<6 s(-1)), and the rate-limiting step appears to be the interprotein electron transfer from heme in QHNDH to the external electron acceptor. Transient kinetic studies of the CTQ-dependent reduction of heme in QHNDH by amine substrates yielded different rate constants for different substrates (72, 190, and 162 s(-1) for methylamine, butylamine, and benzylamine, respectively). Deuterium kinetic isotope effect (KIE) values of 5.3, 3.9, and 8.5 were observed, respectively, for the reactions of methylamine, butylamine, and benzylamine. These results suggest that the abstraction of a proton from the alpha-methylene group of the substrate, which occurs concomitant with CTQ reduction, is the rate-limiting step in the CTQ-dependent reduction of hemes in QHNDH by these amine substrates. In contrast, the reaction of 2-phenylethylamine with QHNDH does not exhibit a significant KIE ((H)k(3)/(D)k(3) = 1.05) and exhibits a much smaller rate constant of 16 s(-1). This suggests that for 2-phenylethylamine, the rate-limiting step in the single-turnover reaction is either hydrolysis of the imine reaction intermediate from CTQ or product release prior to intraprotein electron transfer. Analysis of the products of the reactions of QHNDH with chiral deuterated 2-phenylethylamines demonstrated that the enzyme abstracts the pro-S proton of the substrate in a highly stereospecific manner. Inspection of the crystal structure of phenylhydrazine-inhibited QHNDH suggests that Asp33(gamma) is the residue that performs the proton abstraction. On the basis of these results, kinetic and chemical reaction mechanisms for QHNDH are proposed and discussed in the context of the crystal structure of the enzyme.     

Effects of length and position of an extended linker on sequence-selective DNA recognition of zinc finger peptides

Engineered zinc finger proteins revealed that a linker sequence connecting zinc finger units has a significant effect on the DNA binding property of the protein. The recognition for a noncontiguous DNA target beyond the current recognition code of zinc finger proteins has never been determined because of the limitation of a zinc finger framework. DNA recognition of zinc finger proteins is limited only to a contiguous subset of three base pairs. We propose the recognition for a noncontiguous DNA target by inserting amino acids into the canonical linker between zinc finger units. The sequence selectivity of the new zinc finger peptides was evaluated by gel mobility shift assays. DNase I footprinting analyses clearly showed different DNA binding of various linker-extended zinc finger peptides. The application of a SPR measurement also revealed a DNA sequence selectivity of peptides. Insertion of three amino acids is enough for recognition of a noncontiguous DNA target with sequence selectivity. An extended linker will be useful for expansion of the recognition code of zinc finger proteins and for development of a new role for linker sequences in DNA binding of zinc finger proteins.     

Female multiple mating as a genetic bet-hedging strategy when mate choice criteria are unreliable

Female multiple mating (or polyandry) is considered to act as a genetic bet-hedging mechanism, by which females can reduce the assessment error in regard to mates genetic quality when only uncertain information is available. In spite of frequent verbal arguments, no theoretical examination has been carried out to determine the effectiveness of bet-hedging by multiple mating. In the present paper, I show that three factors, female population size, remating costs and environmental fluctuation, all affect the effectiveness of bet-hedging. A mathematical model predicts that bet-hedging effectively works only in small populations, and computer simulations were used to confirm this prediction. The results of simulations differed according to the degree of environmental fluctuation. In relatively stable environments, if there is no remating cost, the fixation probability of a multiple mating strategy is slightly higher than that of a single mating strategy, independent of female population size. However, with very slight fitness costs, multiple mating drastically loses its advantage as population size increases, and almost always becomes extinct within large populations. This means that the evolution of polyandry solely by the mechanism of bet-hedging is unlikely in stable environments. However, in unpredictable environments, or when negative frequency-dependent selection on fitness-related loci is introduced, a multiple mating strategy is sometimes successful against a single mating strategy, even if it entails a small fitness cost. Therefore, female multiple mating may possibly evolve only in these limited conditions. In most cases, some deterministic mechanisms such as postcopulatory sperm selection by multiply mated females (or direct material benefits) are more reasonable as the evolutionary causes of polyandry.     

Reverse-flow island sural flap

The reverse flow island sural flap is presented as an alternative to flaps currently used for reconstruction of small and medium substance losses in the distal third of the leg, ankle, and heel. This is a random type of flap, based on the reverse flow of the superficial sural artery, which mainly depends on the anatomy of the perforators of the peroneal artery system.The anatomic structures that constitute the pedicle are the superficial and deep fascias, the sural nerve, the short saphenous vein, and the superficial sural artery. The skin island and the subcutaneous cellular tissue complement the flap proper. This skin island was demarcated at any point of the median or distal thirds of the leg, having the short saphenous vein and the sural nerve on its central axis. The distal dissection limit of the pedicle is located 5 centimeters above the lateral malleolus. This limit is established so as to ensure the integrity of the perforators from the principal arteries of the leg, mainly the peroneal artery, responsible for the reverse flow nourishing the flap. These perforators will affect anastomoses with the superficial sural artery in charge of irrigating the structures compounding the flap.A total of 71 patients were operated on with this technique, some of them with basic pathologic abnormalities limiting the distal blood flow, such as diabetes mellitus, and some others having proven vascular insufficiency or displaying unstable areas attributable to problems such as pseudarthrosis and osteomyelitis, which needed to be covered. Fifteen flaps (21.1 percent) suffered partial necrosis, which did not compromise the final result, and another three (4.2 percent) showed total loss. The flap in question has great mobility and versatility, allowing the treatment of specific areas of the lower limb, without sacrificing important arteries or mobilizing structures that might bring about functional deficits.     

A mathematical explanation of an increase in bacterial swimming speed with viscosity in linear-polymer solutions

Bacterial swimming speed is sometimes known to increase with viscosity. This phenomenon is peculiar to bacterial motion. Berg and Turner (Nature. 278:349-351, 1979) indicated that the phenomenon was caused by a loose, quasi-rigid network formed by polymer molecules that were added to increase viscosity. We mathematically developed their concept by introducing two apparent viscosities and obtained results similar to the experimental data reported before. Addition of polymer improved the propulsion efficiency, which surpasses the decline in flagellar rotation rate, and the swimming speed increased with viscosity.     

Gene replacement in mice reveals that the heavily phosphorylated tail of neurofilament heavy subunit does not affect axonal caliber or the transit of cargoes in slow axonal transport

The COOH-terminal tail of mammalian neurofilament heavy subunit (NF-H), the largest neurofilament subunit, contains 44-51 lysine-serine-proline repeats that are nearly stoichiometrically phosphorylated after assembly into neurofilaments in axons. Phosphorylation of these repeats has been implicated in promotion of radial growth of axons, control of nearest neighbor distances between neurofilaments or from neurofilaments to other structural components in axons, and as a determinant of slow axonal transport. These roles have now been tested through analysis of mice in which the NF-H gene was replaced by one deleted in the NF-H tail. Loss of the NF-H tail and all of its phosphorylation sites does not affect the number of neurofilaments, alter the ratios of the three neurofilament subunits, or affect the number of microtubules in axons. Additionally, it does not reduce interfilament spacing of most neurofilaments, the speed of action potential propagation, or mature cross-sectional areas of large motor or sensory axons, although its absence slows the speed of acquisition of normal diameters. Most surprisingly, at least in optic nerve axons, loss of the NF-H tail does not affect the rate of transport of neurofilament subunits.     

<Emphasis Type="Italic">Trichiurus nickolensis</Emphasis>, a new hairtail from Australia belonging to the <Emphasis Type="Italic">Trichiurus russelli</Emphasis> complex (Perciformes: Trichiuridae)

A new hairtail, Trichiurus nickolensis, is described on the basis of ten specimens collected off northwestern Australia, off the Northern Territory, and in the Gulf of Carpentaria, Queensland. The new species strongly resembles T. brevis Wang and You in Wang et al., 1992, off Hainan Island, South China Sea, and T. russelli Dutt and Thankam, 1966, off the Waltair Coast, Andhra Pradesh, India, in having the highest point of the supraoccipital crest situated directly above the posterior margin of the eye and a relatively short caudal peduncle. Trichiurus nickolensis differs from those two species in being strongly pigmented on the anterior section of the dorsal fin membrane (vs. slightly pigmented), and having a dorsal head margin that appears concave in lateral view, rises gently from snout tip to above middle of orbit, and then extends more steeply to dorsal fin origin (vs. rising gently from tip of snout to dorsal fin origin). The new species also has a greater number of dorsal fin rays (III, 138–143 vs. III, 127–132 and III, 127–131 in T. brevis and T. russelli, respectively) and total vertebrae (160–166 vs. 147–155 and 149–153), and shorter preanal length (mean 30% TL vs. 33% TL and 35% TL), head length (11% TL vs. 12% TL and 13% TL) and upper jaw length (4% TL vs. 5% TL and 5% TL).     

Significance of venous anastomosis in fingertip replantation

Adequate venous outflow is the most important factor for successful fingertip replantation. The authors have attempted venous anastomosis in all cases of fingertip replantation to overcome postoperative congestion. In this article, the significance of venous repair for fingertip replantation is described from the authors' results of 64 complete fingertip amputations in 55 consecutive patients, which were replanted from January of 1996 to June of 2001. The overall survival rate was 86 percent. Of the 44 replantations in zone I, 37 survived, and the success rate was 84 percent. Of the 20 replantations in zone II, 18 survived, and the success rate was 90 percent. Venous anastomosis was attempted in all cases, but it was possible in 39 zone I and in all zone II replantations. For arterial repair, vein grafts were necessary in 17 of the 44 zone I and in one of the 20 zone II replantations; for venous repair, they were necessary in six zone I replantations and one zone II replantation. Postoperative vascular complications occurred in 15 replantations. There were five cases of arterial thrombosis and 10 cases of venous congestion. Venous congestion occurred in nine zone I and one zone II replantations. In five of these 10 replantations, venous anastomosis was not possible. In another five replantations, venous outflow was established at the time of surgery, but occlusion occurred subsequently. Except for the five failures resulting from arterial thrombosis, successful venous repair was possible in 49 of 59 replantations (83 percent). Despite the demand for skillful microsurgical technique and longer operation time, the authors' results using venous anastomosis in successful fingertip replantations are encouraging. By performing venous anastomosis, external bleeding can be avoided and a higher survival rate can be achieved. Venous anastomosis for fingertip replantation is a reliable and worthwhile procedure.