Genome sequences of the biotechnologically important Bacillus megaterium strains QM B1551 and DSM319.

Bacillus megaterium is deep-rooted in the Bacillus phylogeny, making it an evolutionarily key species and of particular importance in understanding genome evolution, dynamics, and plasticity in the bacilli. B. megaterium is a commercially available, nonpathogenic host for the biotechnological production of several substances, including vitamin B(12), penicillin acylase, and amylases. Here, we report the analysis of the first complete genome sequences of two important B. megaterium strains, the plasmidless strain DSM319 and QM B1551, which harbors seven indigenous plasmids. The 5.1-Mbp chromosome carries approximately 5,300 genes, while QM B1551 plasmids represent a combined 417 kb and 523 genes, one of the largest plasmid arrays sequenced in a single bacterial strain. We have documented extensive gene transfer between the plasmids and the chromosome. Each strain carries roughly 300 strain-specific chromosomal genes that account for differences in their experimentally confirmed phenotypes. B. megaterium is able to synthesize vitamin B(12) through an oxygen-independent adenosylcobalamin pathway, which together with other key energetic and metabolic pathways has now been fully reconstructed. Other novel genes include a second ftsZ gene, which may be responsible for the large cell size of members of this species, as well as genes for gas vesicles, a second ß-galactosidase gene, and most but not all of the genes needed for genetic competence. Comprehensive analyses of the global Bacillus gene pool showed that only an asymmetric region around the origin of replication was syntenic across the genus. This appears to be a characteristic feature of the Bacillus spp. genome architecture and may be key to their sporulating lifestyle.

Halide coordination of perhalocyclohexasilane Si6X12 (X=Cl or Br).

The addition of halide anions (X' = Cl(-), Br(-), or I(-)) to perhalocyclohexasilane Si(6)X(12) (X = Cl or Br) led to the formation of complexes comprising [Si(6)X(12)X'(2)](2-) dianions. An upfield shift in the (29)Si NMR spectra was noted upon coordination, and structural determination by X-ray crystallography showed that the dianions adopt an "inverse sandwich" structure where the six cyclic silicon atoms form a planar hexagon with the two halide anions X' located on the 6-fold axis equally disposed above and below the plane of the Si(6) ring. Additionally, these apical X' atoms are within the van der Waals bonding distance to the silicon ring atoms, indicating a strong interaction between X' and silicon atoms. These results detail crystallographic variations within the halogen series providing further insight into the nature of the Lewis acid sites above and below the Si(6)X(12) ring, where interactions with hard Lewis bases such as halide anions are observed. Interestingly, the stereochemistry of the silicon atoms in [Si(6)X(12)X'(2)](2-) is not affected much by the size or electronegativity of the halogen atoms.

The detection of pressure fluctuations, sonic audition, is the dominant mode of dipole-source detection in goldfish (Carassius auratus).

Behavioral detection of a low-frequency (40 Hz) vibratory dipole at source distances of 1.5-24 cm was measured by classically conditioned respiratory suppression in goldfish (Carassius auratus). Detection thresholds were compared across distances and before and after ablation of individual octavolateralis sensory channels. Detection thresholds, expressed in units of pressure (SPL), remained roughly constant as distance between the stimulus source and animal increased. Lateral line inactivation, using CoCl2, had no measurable effect on sensitivity, although some other results can be construed as weak evidence for a small contribution of the lateral line to dipole detection when source distances are

A JAR of Chirps: The Gymnotiform Chirp Can Function as Both a Communication Signal and a Jamming Avoidance Response.

The weakly electric gymnotiform fish produce a rhythmic electric organ discharge (EOD) used for communication and active electrolocation. The EOD frequency is entrained to a medullary pacemaker nucleus. During communication and exploration, this rate can be modulated by a pre-pacemaker network, resulting in specific patterns of rate modulation, including stereotyped communication signals and dynamic interactions with conspecifics known as a Jamming Avoidance Response (JAR). One well-known stereotyped signal is the chirp, a brief upward frequency sweep usually lasting less than 500 ms. The abrupt change in frequency has dramatic effects on phase precession between two signalers. We report here on chirping in Brachyhypopmus cf. sullivani, Microsternarchus cf. bilineatus Lineage C, and Steatogenys cf. elegans during conspecific playback experiments. Microsternarchus also exhibits two behaviors that include chirp-like extreme frequency modulations, EOD interruptions with hushing silence and tumultuous rises, and these are described in terms of receiver impact. These behaviors all have substantial impact on interference caused by conspecifics and may be a component of the JAR in some species. Chirps are widely used in electronic communications systems, sonar, and other man-made active sensing systems. The brevity of the chirp, and the phase disruption it causes, makes chirps effective as attention-grabbing or readiness signals. This conforms to the varied assigned functions across gymnotiforms, including pre-combat aggressive or submissive signals or during courtship and mating. The specific behavioral contexts of chirp expression vary across species, but the physical structure of the chirp makes it extremely salient to conspecifics. Chirps may be expected in a wide range of behavioral contexts where their function depends on being noticeable and salient. Further, in pulse gymnotiforms, the chirp is well structured to comprise a robust jamming signal to a conspecific receiver if specifically timed to the receiver's EOD cycle. Microsternarchus and Steatogenys exploit this feature and include chirps in dynamic jamming avoidance behaviors. This may be an evolutionary re-use of a circuitry for a specific signal in another context.

Objective threshold estimation and measurement of the residual background noise in auditory evoked potentials of goldfish.

A survey of papers using auditory evoked potentials (AEPs) published over the last 10 years (Table I) demonstrates that most AEP studies in animals have used subjective methods for auditory threshold determination. Subjective methods greatly reduce the value of statistical hypothesis testing and jeopardize tests of hypothetical experimental group differences in hearing sensitivity. Correspondingly, many attempts have been made to develop objective threshold determination methods, but these have not been used widely. Further, they seldom include an appreciation of the effects of residual noise in the AEP. In this study, AEPs evoked by tonal and noise stimuli in goldfish (Carassius auratus) were recorded and the residual background noise was measured and analyzed in detail. High variability was found in residual noise, but can be effectively controlled with a simple modification of averaging routines. Considerable interobserver disagreements were found using subjective threshold estimation. An objective method of threshold determination was developed based on comparison between AEP amplitude and controlled residual noise, using a signal detection theory approach to set specific threshold criteria. The usefulness of AEP in hypothesis testing for auditory function requires more control over residual background noise amplitudes and the use of objective threshold determination techniques.

The use of anesthesia during evoked potential audiometry in goldfish (Carassius auratus).

Auditory-evoked potentials (AEPs) have become a widely utilized measure of hearing sensitivity. Most investigators use pharmacological paralysis to reduce myogenic noise and immobilize the animal for stable electrical recordings, but additional anesthesia is generally not used because the most commonly available fish anesthetic, the cholinergic antagonist tricaine methanosulfate (MS222), is known to disrupt hair cell and primary afferent physiology. Anesthetic agents that do not interfere with auditory function would be a useful adjunct to paralytic immobilization and would reduce any possible distress incurred by prolonged immobilization. In this report we tested the opiate anesthetic fentanyl and compared hearing thresholds in immobilized versus immobilized and anesthetized animals. Short-term effects of mild MS222 anesthesia were also measured via evoked potential audiometry. Animals were tested before and after fentanyl injection (100, 500 and 2500 microg g(-1) fish body-weight) using standard evoked potential audiometry. Tone pips, 0.2-3 kHz, from an aerial loudspeaker served as stimuli. Fentanyl altered evoked potential waveforms slightly but did not alter estimated threshold sensitivity. These results suggest fentanyl be considered as a possible addition to AEP techniques in goldfish (Carassius auratus) and poikilothermic vertebrates generally.

The hydrodynamic footprint of a benthic, sedentary fish in unidirectional flow.

Mottled sculpin (Cottus bairdi) are small, benthic fish that avoid being swept downstream by orienting their bodies upstream and extending their large pectoral fins laterally to generate negative lift. Digital particle image velocimetry was used to determine the effects of these behaviors on the spatial and temporal characteristics of the near-body flow field as a function of current velocity. Flow around the fish's head was typical for that around the leading end of a rigid body. Flow separated around the edges of pectoral fin, forming a wake similar to that observed for a flat plate perpendicular to the flow. A recirculation region formed behind the pectoral fin and extended caudally along the trunk to the approximate position of the caudal peduncle. In this region, the time-averaged velocity was approximately one order of magnitude lower than that in the freestream region and flow direction varied over time, resembling the periodic shedding of vortices from the edge of a flat plate. These results show that the mottled sculpin pectoral fin significantly alters the ambient flow noise in the vicinity of trunk lateral line sensors, while simultaneously creating a hydrodynamic footprint of the fish's presence that may be detected by the lateral line of nearby fish.

Long-term changes in ground water chemistry at a phytoremediation demonstration site.

A field-scale demonstration project was conducted to evaluate the capability of eastern cottonwood trees (Populus deltoides) to attenuate trichloroethene (TCE) contamination of ground water. By the middle of the sixth growing season, trees planted where depth to water was <3 m delivered enough dissolved organic carbon to the underlying aquifer to lower dissolved oxygen concentrations, to create iron-reducing conditions along the plume centerline and sulfate-reducing or methanogenic conditions in localized areas, and to initiate in situ reductive dechlorination of TCE. Apparent biodegradation rate constants for TCE along the centerline of the plume beneath the phytoremediation system increased from 0.0002/d to 0.02/d during the first six growing seasons. The corresponding increase in natural attenuation capacity of the aquifer along the plume centerline, from 0.0004/m to 0.024/m, is associated with a potential decrease in plume-stabilization distance from 9680 to 160 m. Demonstration results provide insight into the amount of vegetation and time that may be needed to achieve cleanup objectives at the field scale.

Signals and noise in the octavolateralis systems: what is the impact of human activities on fish sensory function?

The octavolateralis systems of fishes include the vestibular, auditory, lateral line and electrosensory systems. They are united by common developmental and neuro-computational features, including hair cell sensors and computations based on cross-neuron analyses of differential hair cell stimulation patterns. These systems also all use both spectral and temporal filters to separate signals from each other and from noise, and the distributed senses (lateral line and electroreception) add spatial filters as well. Like all sensory systems, these sensors must provide the animal with guidance for adaptive behavior within a sensory scene composed of multiple stimuli and varying levels of ambient noise, including that created by human activities. In the extreme, anthropogenic activities impact the octavolateralis systems by destroying or degrading the habitats that provide ecological resources and sensory inputs. At slightly lesser levels of effect, anthropogenic pollutants can be damaging to fish tissues, with sensory organs often the most vulnerable. The exposed sensory cells of the lateral line and electrosensory systems are especially sensitive to aquatic pollution. At still lesser levels of impact, anthropogenic activities can act as both acute and chronic stressors, activating hormonal changes that may affect behavioral and sensory function. Finally, human activities are now a nearly ubiquitous presence in aquatic habitats, often with no obvious effects on the animals exposed to them. Ship noise, indigenous and industrial fishing techniques, and all the ancillary noises of human civilization form a major part of the soundscape of fishes. How fish use these new sources of information about their habitat is a new and burgeoning field of study.

Contributions of dysregulated energy metabolism to type 2 diabetes development in NZO/H1Lt mice with polygenic obesity.

New Zealand Obese (NZO) male mice develop a polygenic juvenile-onset obesity and maturity-onset hyperinsulinemia and hyperglycemia (diabesity). Here we report on metabolic and molecular changes associated with the antidiabesity action of CL316,243 (CL), a beta(3)-adrenergic receptor agonist. Dietary CL treatment initiated at weaning reduced the peripubertal rise in body weight and adiposity while promoting growth without suppressing hyperphagia. The changes in adiposity, in turn, suppressed development of hyperinsulinemia, hyperleptinemia, hyperlipidemia, and hyperglycemia. These CL-induced alterations were reflected by decreased adipose tissue mass, increased expression of transcripts for uncoupling protein-1 (UCP-1), peroxisome proliferator-activated receptor alpha (PPARalpha), peroxisome proliferater-activated receptor coactivator-1 (PGC-1), and robust development of brown adipocyte function in white fat. Increased drug-mediated energy dissipation elicited a 1.5 degrees C increase in whole body temperature under conditions of increased food intake but with no change in physical activity. Indirect calorimetry of mice treated with CL showed both increased energy expenditure and a restoration of a prominent diurnal pattern in the respiratory exchange ratio suggesting improved nutrient sensing. Our data suggest that CL promotes increased energy dissipation in white and brown fat depots by augmenting thermogenesis and by metabolic re-partitioning of energy in a diabesity-protective fashion. This is the first report demonstrating the effects of dietary beta(3)-agonist in preventing the onset of diabesity in a polygenic rodent model of type 2 diabetes.

Volatilization of polycyclic aromatic hydrocarbons from coal-tar-sealed pavement.

Coal-tar-based pavement sealants, a major source of PAHs to urban water bodies, are a potential source of volatile PAHs to the atmosphere. An initial assessment of volatilization of PAHs from coal-tar-sealed pavement is presented here in which we measured summertime gas-phase PAH concentrations 0.03 m and 1.28 m above the pavement surface of seven sealed (six with coal-tar-based sealant and one with asphalt-based sealant) and three unsealed (two asphalt and one concrete) parking lots in central Texas. PAHs also were measured in parking lot dust. The geometric mean concentration of the sum of eight frequently detected PAHs (ΣPAH(8)) in the 0.03-m samples above sealed lots (1320 ng m(-3)) during the hottest part of the day was 20 times greater than that above unsealed lots (66.5 ng m(-3)). The geometric mean concentration in the 1.28-m samples above sealed lots (138 ng m(-3)) was five times greater than above unsealed lots (26.0 ng m(-3)). Estimated PAH flux from the sealed lots was 60 times greater than that from unsealed lots (geometric means of 88 and 1.4 µg m(-2) h(-1), respectively). Although the data set presented here is small, the much higher estimated fluxes from sealed pavement than from unsealed pavement indicate that coal-tar-based sealants are emitting PAHs to urban air at high rates compared to other paved surfaces.

Perception of frequency, amplitude, and azimuth of a vibratory dipole source by the octavolateralis system of goldfish (Carassius auratus).

Goldfish (Carassius auratus) were conditioned to suppress respiration to a 40-Hz vibratory source and subsequently tested for stimulus generalization to frequency, stimulus amplitude, and position (azimuth). Animals completely failed to generalize to frequencies separated by octave intervals both lesser and greater than the CS. However, they did appear to generalize weakly to an aerial loudspeaker stimulus of the same frequency (40 Hz) after conditioning with an underwater vibratory source. Animals had a gradually decreasing amount of generalization to amplitude changes, suggesting a perceptual dimension of loudness. Animals generalized largely or completely to the same underwater source presented at a range of source azimuths. When these azimuths were presented at a transect of 3 cm, some animals did show decrements in generalization, while others did not. This suggests that although azimuth may be perceived more saliently at distances closer to a dipole source, perception of position is not immediately salient in conditioned vibratory source detection. Differential responding to test stimuli located toward the head or tail suggests the presence of perceptual differences between sources that are rostral or caudal with respect to the position of the animal or perhaps the head.

Vibratory sources as compound stimuli for the octavolateralis systems: dissection of specific stimulation channels using multiple behavioral approaches.

Underwater vibratory sources simultaneously present acoustic and hydrodynamic disturbances. Because vibratory dipole sources are poor sonic projectors, most researchers have assumed that such sources are of greatest relevance to the lateral line system. Both hydroacoustic principles and empirical studies have shown that dipole sources are also a potent stimulus to the inner ear. Responses to vibratory sources in mottled sculpin (Cottus bairdi) were assessed using unconditioned orienting, differential and nondifferential conditioning. Orienting responses are dominated by lateral line inputs and eliminated by lateral line inactivation. Simple conditioning depends on inputs from other systems and was not affected by lateral line inactivation. Differential conditioning alters behavioral control, and sculpin could be conditioned to ignore substrate-borne vibrations and respond only to hydroacoustic stimulation of the ear. The lateral line and inner ear of mottled sculpin do not necessarily exhibit range fractionation, as both systems operate over a similar distance (within 1.5 body lengths) and respond to many of the same sources. Vibratory dipole sources generate compound stimuli that simultaneously activate multiple octavolateralis systems, and sculpin make use of the channels differentially under different behavioral tasks.

Binge ethanol treatment causes greater brain damage in alcohol-preferring P rats than in alcohol-nonpreferring NP rats.

BACKGROUND: Genetics is a known risk factor for alcoholism, and human alcoholics are known to suffer from a loss of brain function and mass. A 4 day rat binge drinking model is known to cause brain region-specific damage. To investigate the role of genetics in binge-drinking-induced brain damage, we studied bidirectionally selected rat lines, the alcohol-preferring P and the alcohol-nonpreferring NP rat lines. METHOD: P and NP rats were treated with a 4 day binge ethanol protocol. Animals were killed, transcardially perfused, and fixed, and their brains were removed, sectioned, and stained by using the amino cupric silver stain of de Olmos or by using immunohistochemistry for phospho-extracellular signal regulated kinases and other antigens. RESULTS: Significant brain damage was found in the olfactory bulbs, posterior perirhinal cortex, and entorhinal cortex in both P and NP rats. P rats were found to have significantly greater brain damage, compared with NP rats, in the posterior perirhinal and posterior entorhinal cortexes, 239% +/- 50% (p < 0.02) and 219% +/- 46% (p < 0.01), respectively. Phospho-extracellular signal regulated kinase immunohistochemistry stained prominently in damaged brain areas. CONCLUSIONS: The P rat line, a genetic model of alcoholism, shows greater region-specific brain damage due to binge ethanol treatment than its genetic counterpart, the NP rat line. These findings suggest that genetics contribute to susceptibility for binge-induced brain damage.

What is the nature of multisensory interaction between octavolateralis sub-systems?

The octavolateralis system consists of several submodalities, including the inertial-sensitive inner ear, the pressure-sensitive ear/air cavity complex (when present), and acceleration- and velocity-sensitive components of the lateral line system (canal and superficial neuromasts, respectively). All four of these channels are responsive to many of the same stimulus sources, particularly moving or vibrating objects within a short distance from the receiver. We therefore argue that the octavolateralis system is an excellent model for the study of multisensory interactions. We focus on the possible ways in which these channels may contribute to source localization mechanisms and to the multisensory guidance of behaviors with strong directional components (e.g., predator avoidance, prey capture and mate attraction). Finally, we define four ways in which information from multiple senses might interact. These include fractionation, synergy, accessory stimulation, and complementation. Although evidence for all types of octavolateralis interactions can be found, the primary modes of interaction appear to be complementation and fractionation. For example, the inertial and pressure-sensitive submodalities of the auditory system provide complementary pieces of information about the direction (e.g., left/right) and polarity (advancing or receding) of a moving source. In contrast, the lateral line canal system subserves short-range localization tasks, whereas the auditory system may subserve longer-range detection and localization tasks.