Functional Gene Hybridization Patterns of Terrestrial Ammonia-Oxidizing Bacteria

Abstract The biochemical pathway and genetics of autotrophic ammonia oxidation have been studied almost exclusively in Nitrosomonas europaea. Terrestrial autotrophic ammonia-oxidizing bacteria (AAOs), however, comprise two distinct phylogenetic groups in the beta-Proteobacteria, the Nitrosomonas and Nitrosospira groups. Hybridization patterns were used to assess the potential of functional probes in non-PCR-based molecular analysis of natural AAO populations and their activity. The objective of this study was to obtain an overview of functional gene homologies by hybridizing probes derived from N. europaea gene sequences ranging in size from 0.45 to 4.5 kb, and labeled with 32P to Southern blots containing genomic DNA from four Nitrosospira representatives. Probes were specific for genes encoding ammonia monooxygenase (amoA and amoB), hydroxylamine oxidoreductase (hao), and cytochrome c-554 (hcy). These probes produced hybridization signals, at low stringency (30 degreesC), with DNA from each of the four representatives; signals at higher stringency (42 degreesC) were greatly reduced or absent. The hybridization signals at low stringency ranged from 20 to 76% of the total signal obtained with N. europaea DNA. These results indicate that all four functional genes in the ammonia oxidation pathway have diverged between the Nitrosomonas and Nitrosospira groups. The hao probe produced the most consistent hybridization intensities among the Nitrosospira representatives, suggesting that hao sequences would provide the best probes for non-PCR-based molecular analysis of terrestrial AAOs. Since N. europaea can also denitrify, an additional objective was to hybridize genomic DNA from AAOs with probes for Pseudomonas genes involved in denitrification. These probes were specific for genes encoding heme-type dissimilatory nitrite reductase (dNir), Cu-type dNir, and nitrous oxide reductase (nosz). No hybridization signals were observed from probes for the heme-type dNir or nosz, but Nitrosospira sp. NpAV and Nitrosolobus sp. 24-C hybridized, under low-stringency conditions, with the Cu-type dNir probe. These results indicate that AAOs may also differ in their mechanisms and capacities for denitrification.     

Patterns of differentiation and hybridization in North American wolflike canids, revealed by analysis of microsatellite loci

Genetic divergence and gene flow among closely related populations are difficult to measure because mutation rates of most nuclear loci are so low that new mutations have not had sufficient time to appear and become fixed. Microsatellite loci are repeat arrays of simple sequences that have high mutation rates and are abundant in the eukaryotic genome. Large population samples can be screened for variation by using the polymerase chain reaction and polyacrylamide gel electrophoresis to separate alleles. We analyzed 10 microsatellite loci to quantify genetic differentiation and hybridization in three species of North American wolflike canids. We expected to find a pattern of genetic differentiation by distance to exist among wolflike canid populations, because of the finite dispersal distances of individuals. Moreover, we predicted that, because wolflike canids are highly mobile, hybrid zones may be more extensive and show substantial changes in allele frequency, relative to nonhybridizing populations. We demonstrate that wolves and coyotes do not show a pattern of genetic differentiation by distance. Genetic subdivision in coyotes, as measured by theta and Gst, is not significantly different from zero, reflecting persistent gene flow among newly established populations. However, gray wolves show significant subdivision that may be either due to drift in past Ice Age refugia populations or a result of other causes. Finally, in areas where gray wolves and coyotes hybridize, allele frequencies of gray wolves are affected, but those of coyotes are not. Past hybridization between the two species in the south-central United States may account for the origin of the red wolf.      

Acoustic irradiation produced by flying moths (Lepidoptera,Noctuidae)

Characteristics of acoustic waves accompanying the flight of noctuid moths (Noctuidae) were measured. The low-frequency part of the spectrum is formed of a series of up to 17 harmonics of the wingbeat frequency (30–50 Hz) with a general tendency toward the decrease in the spectral density and the increase in the sound frequency. The root-mean-square level of the sound pressure from flapping wings was found to be 70–78 dB SPL. Besides low-frequency components, the flight of moths was accompanied by short ultrasonic pulses, which appeared with every wingbeat. Most of the spectral energy was concentrated within a range of 7–150 kHz with the main peaks at 60–110 kHz. The short-term pulses were divided into two or more subpulses with different spectra. The high-frequency pulses were produced at two phases of the wingbeat cycle: during the pronation of the wings at the highest point and at the beginning of their upward movement from the lowest point. In most of the specimens tested, the peak amplitude of sounds varied from 55 to 65 dB SPL at a distance of 6 cm from the insect body. However, in nine noctuid species, no high-frequency acoustic components were recorded. In these experiments, the acoustic flow from the flying moth within a frequency range of 2 to 20 kHz did not exceed the self-noise level of the microphone amplifier (RMS 18 dB SPL). Probable mechanisms of the high frequency acoustic emission during flight, the effect of these sounds on the auditory sensitivity of moths, and the possibility of their self-revealing to insectivorous bats are discussed. In addition, spectral characteristics of the moth echolocation clicks were more precisely determined within the higher frequency range (>100 kHz).     

Functional activity of transposase of Bordetella pertussis IS element in Escherichia coli cells

An Escherichia coli strain producing transposase of a repeated sequence of Bordetella pertussis chromosome (RSBP) was constructed. A defective MGE-helper plasmid method, which allowed the determination of transposase functional activity was developed. It was shown that transposase synthesized in E. coli cells ensures transposition of "defective" RSBP into the host chromosome. Overexpression of transposase was shown to markedly decrease the vital activity of E. coli cells under selective cultivation conditions. Reasons for a decrease in viability transposase-producing cells are discussed. Results showing the impact of transposase on replication of recombinant plasmids and E. coli cell division were obtained.     

Comparative study of the rod and cone contributions to the generation of b-wave ERG and tectal evoked potential in the dark-adapted carp

Amplitudes and peak latencies as functions of wave length and monochromatic light intensity were investigated for b-wave ERG and tectal evoked potentials (EP) in the dark-adapted carp (Cyprinus carpio L). It was found, that independently of light intensity b-wave action spectra had one maximum in the medium wave band, corresponding to rod sensitivity area. For tectal EP, similar action spectra with maximum in the middle-wave were seen at low light intensity only. The b-wave amplitude growth was significant for the whole band of light intensities, and these changes were accompanied with a slight decrease in peak latency (to 50-100 ms). Tectal EP amplitude increased when low-intensity light was changed for medium intensity light and did not considerably increase to brighter light stimuli. However, tectal EP time latency significantly decreased (to 100-200 ms) during light intensity increasing. This differences show that retinal rod system, which in responsible for ERG b-wave in darkness, is not a key factor in the generation of tectal EP.     

A preliminary method for estimating the age of brown kiwi (Apteryx mantelli) embryos

Morphological features of a collection of unknown-age wild kiwi (Apteryx mantelli) embryos from early development to point of hatch are described. Using these features, we assign developmental stages to each embryo and compare the progress of development to similar-staged ostrich (Struthio camelus) and chicken (Gallus gallus) embryos. Two ageing schemes for the kiwi embryos are developed by comparing measurements of their hindlimb segments, bills and crown–rump lengths with those of ostrich and chicken embryos at various stages of development. One of the 20 kiwi embryos was of known age. Both the ostrich model and the chicken model gave identical predictions for the marker and four other embryos. Developmental timing of some features differed between all three species, most markedly in the bill, with growth in the kiwi bill being relatively faster to achieve its larger relative and absolute size at hatch.     

Specific features of photorespiration in photosynthetically active organs of C3 plants

Photorespiration of photosynthetically active organs of C₃ plants (leaf, ear, stem, and leaf sheath) and C₄ plants (leaf, tassel, stem, leaf sheath, ear husk) grown under greenhouse and field conditions was studied. Photorespiration was measured using a PTM-48A high-technology monitor of photosynthesis (Bioinstruments S.R.L., Moldova). It is shown that photorespiration (CO₂ ejection after light turning off — apparent photorespiration) in C₃ plants is characteristic only for their leaves. In other photosynthesizing organs, photorespiration was absent, like in the photosynthesizing organs of C₄ plants. The absence of such after-light CO₂ outburst was observed for 31 genotypes: 18 cereal species belonging to four species (Triticum aestivum L., T. durum Desf., Secale cereale L., and Triticale); 6 grain legumes belonging to 2 species (Pisum sativum L. and Glycine max L.); 7 species of wild and rarely cultivated genotypes (T. boeoticum Boiss., T. dicoccoides Koern., T. dicoccum Schuebl., T. spelta L., T. compactum Host., T. monococcum L., and T. sphaerococcum Persiv.), and 2 genotypes of C₄ plants (Zea mays L. and Sorgum vulgaris L.). In all tested photosynthetically active genotypes, except of the C₃ plant leaves, apparent photorespiration was absent, but rather active glycolate cycle operated. The activity of this cycle was determined from the activity of the key enzyme of this cycle — glycolate oxidase. It was supposed that C₃ plants have two mechanisms of CO₂ assimilation: the first one — the mechanism of C₃ type localized in the leaves and the second one localized in other photosynthesizing organs, similar or with some elements of C₄ mechanism of CO₂ assimilation, limiting after-light CO₂ ejection during the metabolism of glycolate.     

Characterization of the deoxynucleotide triphosphate triphosphohydrolase (dNTPase) activity of the EF1143 protein from Enterococcus faecalis and crystal structure of the activator-substrate complex

The EF1143 protein from Enterococcus faecalis is a distant homolog of deoxynucleotide triphosphate triphosphohydrolases (dNTPases) from Escherichia coli and Thermus thermophilus. These dNTPases are important components in the regulation of the dNTP pool in bacteria. Biochemical assays of the EF1143 dNTPase activity demonstrated nonspecific hydrolysis of all canonical dNTPs in the presence of Mn(2+). In contrast, with Mg(2+) hydrolysis required the presence of dGTP as an effector, activating the degradation of dATP and dCTP with dGTP also being consumed in the reaction with dATP. The crystal structure of EF1143 and dynamic light scattering measurements in solution revealed a tetrameric oligomer as the most probable biologically active unit. The tetramer contains four dGTP specific allosteric regulatory sites and four active sites. Examination of the active site with the dATP substrate suggests an in-line nucleophilic attack on the α-phosphate center as a possible mechanism of the hydrolysis and two highly conserved residues, His-129 and Glu-122, as an acid-base catalytic dyad. Structural differences between EF1143 apo and holo forms revealed mobility of the α3 helix that can regulate the size of the active site binding pocket and could be stabilized in the open conformation upon formation of the tetramer and dGTP effector binding.