Species Richness and Invasion Vectors: Sampling Techniques and Biases

During a European Union Concerted Action study on species introductions, an intercalibration workshop on ship ballast water sampling techniques considered various phytoplankton and zooplankton sampling methods. For the first time, all the techniques presently in use worldwide were compared using a plankton tower as a model ballast tank spiked with the brine shrimp and oyster larvae while phytoplankton samples were taken simultaneously in the field (Helgoland Harbour, Germany). Three cone-shaped and 11 non-cone shaped plankton nets of different sizes and designs were employed. Net lengths varied from 50 to 300 cm, diameters 9.7–50 cm, and mesh sizes 10–100 μm. Three pumps, a Ruttner sampler, and a bucket previously used in ballast water sampling studies were also compared. This first assessment indicates that for sampling ballast water a wide range of techniques may be needed. Each method showed different results in efficiency and it is unlikely that any of the methods will sample all taxa. Although several methods proved to be valid elements of a hypothetical `tool box' of effective ship sampling techniques. The Ruttner water sampler and the pump P30 provide suitable means for the quantitative phytoplankton sampling, whereas other pumps prevailed during the qualitative trial. Pump P15 and cone-shaped nets were the best methods used for quantitative zooplankton sampling. It is recommended that a further exercise involving a wider range of taxa be examined in a larger series of mesocosms in conjunction with promising treatment measures for managing ballast water. This revised version was published online in July 2006 with corrections to the Cover Date.     

Directionality of the tympanal vibrations in a cicada: a biophysical analysis

1. Laser vibrometry and acoustic measurements were used to study the biophysics of directional hearing in males and females of a cicada, in which most of the male tympanum is covered by thick, water filled tissue “pads”. 2. In females, the tympanal vibrations are very dependent on the direction of sound incidence in the entire frequency range 1–20 kHz, and especially at the main frequencies of the calling song (3–7 kHz). At frequencies up to 10 kHz, the directionality disappears if the contralateral tympanum, metathoracic spiracle, and folded membrane are blocked with Vaseline. This suggests some pressure-difference receiver properties in the ear. 3. In males, the tympanal vibrations depend on the direction of sound incidence only within narrow frequency bands (around 1.8 kHz and at 6–7 kHz). At frequencies above 10–12 kHz, the directionality appears to be determined by diffraction, and the ear seems to work as a pressure receiver. The peak in directionality at 6–7 kHz disappears when the contralateral timbal, but not the tympanum, is covered. Covering the thin ventral abdominal wall causes the peak around 1.8 kHz to disappear. 4. Most observed tympanal directionalities, except around 1.8 kHz in males, are well predicted from measured transmissions of sound through the body and measured values of sound amplitude and phase at the ears at various directions of sound incidence. Accepted: 18 October 1996     

An autoregressive method for the measurement of synchronization of interictal and ictal EEG signals

We propose a new measure of synchronization of multichannel ictal and interictal EEG signals. The measure is based on the residual covariance matrix of a multichannel autoregressive model. A major advantage of this measure is its ability to be interpreted both in the framework of stochastic and deterministic models. A preliminary analysis of EEG data from three patients using this measure documents the expected increased synchronization during ictal periods but also reveals that increased synchrony persists for prolonged periods (up to 2 h or more) in the postictal period. Received: 20 July 1997 / Accepted in revised form: 26 January 1999     

Disposable sensor for measuring the biochemical oxygen demand for nitrification and inhibition of nitrification in wastewater

A disposable-type microbial sensor was developed for the determination of both the biochemical oxygen demand for nitrification (N-BOD) and inhibiting effects on nitrifying bacteria. The sensor was based on the respiratory activity of nitrifying bacteria immobilized on a miniature oxygen electrode. Typical response times for measuring N-BOD of ammonium standard solutions as well as of wastewater samples were in the range of 6–12 min. A dynamic evaluation of the signals after a measuring time of 120 s also resulted in good reproducibility and sensitivity. A daily profile of a municipal sewage plant was recorded, comparing the biosensor data with two standard methods. For the measurement of nitrification-inhibiting effects a 120-s dynamic signal evaluation was preferred to a steady-state method because of the long recovery times resulting from extended exposure to inhibitors. However, steady-state measurement techniques allowed allylthiourea detection with a ten times higher sensitivity. Because of the advantages of this miniaturized electrode, e.g. short response time, simple measuring procedure and low costs of production, this sensor system is considered to be suitable for commercial application in environmental analysis. Received: 30 April 1998 / Received revision: 4 September 1998 / Accepted: 13 September 1998     

An architectural hypothesis for direction selectivity in the visual cortex: the role of spatially asymmetric intracortical inhibition

Within a linear field approach, an architectural model for simple cell direction selectivity in the visual cortex is proposed. The origin of direction selectivity is related to recurrent intracortical interactions with a spatially asymmetric character along the axis of stimulus motion. No explicit asymmetric temporal mechanisms are introduced or adopted. The analytical investigation of network behavior, carried out under the assumption of a linear superposition of geniculate and intracortical contributions, shows that motion sensitivity of the resulting receptive fields emerges as a dynamic property of the cortical network without any feed-forward direction selectivity bias. A detailed analysis of the effects of the architectural characteristics of the cortical network on directionality and velocity-response curves was conducted by systematically varying the model's parameters. Received: 8 May 1998 / Accepted in revised form: 10 November 1998     

Simulation of the packing of idealized transmembrane α-helix bundles

The aim of this study is to investigate if the packing motifs of native transmembrane helices can be produced by simulations with simple potentials and to develop a method for the rapid generation of initial candidate models for integral membrane proteins composed of bundles of transmembrane helices. Constituent residues are mapped along the helix axis in order to maintain the amino acid sequence-dependent properties of the helix. Helix packing is optimized according to a semi-empirical potential mainly composed of four components: a bilayer potential, a crossing angle potential, a helix dipole potential and a helix-helix distance potential. A Monte Carlo simulated annealing protocol is employed to optimize the helix bundle system. Necessary parameters are derived from theoretical studies and statistical analysis of experimentally determined protein structures. Preliminary testing of the method has been conducted with idealized seven Ala₂₀ helix bundles. The structures generated show a high degree of compactness. It was observed that both bacteriorhodopsin-like and δ-endotoxin-like structures are generated in seven-helix bundle simulations, within which the composition varies dependent upon the cooling rate. The simulation method has also been employed to explore the packing of N = 4 and N = 12 transmembrane helix bundles. The results suggest that seven and 12 transmembrane helix bundles resembling those observed experimentally (e.g., bacteriorhodopsin, rhodopsin and cytochrome c oxidase subunit I) may be generated by simulations using simple potentials. Received: 16 November 1998 / Revised version: 26 March 1999 / Accepted: 8 April 1999     

Visual acuity, contrast sensitivity and retinal magnification in a marsupial, the tammar wallaby (Macropus eugenii )

The visual acuity of the tammar wallaby was estimated using a behavioural discrimination task. The wallabies were trained to discriminate a high-contrast (86%) square-wave grating from a grey field of equal luminance (1000–6000 cd m⁻²). Visual-evoked cortical potentials were used to measure the complete contrast sensitivity function. The stimulus was a sinusoidal phase reversal of a sinusoidally modulated grating of various spatial frequencies and contrasts with a mean luminance of 40 cd m⁻². The behavioural acuity was estimated to be about 4.8 cycles/deg. The contrast sensitivity peaked at about 0.15 cycles/deg and declined towards both lower and higher spatial frequencies. The cut-off frequency of the contrast sensitivity function is slightly lower than the behaviourally measured acuity at about 2.7 cycles/deg. The retinal magnification factor was estimated anatomically from laser lesions to be about 0.16 mm/deg. Based on the known ganglion cell density and the retinal magnification factor, an anatomical upper limit to visual acuity of about 6 cycles/deg can be calculated. The differences in estimates of visual acuity between the behavioural and anatomical methods on the one side and physiology on the other side are discussed. Accepted: 28 May 1998     

Production of ketocarotenoids by microalgae

Among the highly valued ketocarotenoids employed for food coloration, astaxanthin is probably the most important. This carotenoid may be produced biotechnologically by a number of microorganisms, and the most promising seems to be the freshwater flagellate Haematococcus pluvialis (Chlorophyceae), which accumulate astaxanthin in their aplanospores. Many physiological aspects of the transition of the flagellate into aplanospores have been described. Mixotrophic cultivation and suitable irradiance may result in fairly good yields (up to 40 mg/l; 43 mg/g cell dry weight) within a reasonable time, under laboratory conditions. In order to compete with synthetic astaxanthin, suitable scaling-up is required. However, large-scale production in open ponds has proved unsatisfactory because of severe contamination problems. A selective medium might overcome this difficulty. Further research for the development of suitable strains is thus warranted. Received: 8 July 1998 / Received revision: 12 November 1998 / Accepted: 14 November 1998     

Directionality of auditory nerve fiber responses to pure tone stimuli in the grassfrog, Rana temporaria. I. Spike rate responses

We studied the directionality of spike rate responses of auditory nerve fibers of the grassfrog, Rana temporaria, to pure tone stimuli. All auditory fibers showed spike rate directionality. The strongest directionality was seen at low frequencies (200 – 400 Hz), where the spike rate could change by up to nearly 200␣spikes s⁻¹. with sound direction. At higher frequencies the directional spike rate changes were mostly below 100 spikes s⁻¹. In equivalent dB SPL terms (calculated using the fibers' rate-intensity curves) the maximum directionalities were up to 15 dB at low frequencies and below 10 dB at higher frequencies. Two types of directional patterns were observed. At frequencies below 500 Hz relatively strong responses were evoked by stimuli from the ipsilateral (+90^o) and contralateral (−90^o) directions while the weakest responses were evoked by stimuli from frontal (0^o or +30^o) or posterior (−135^o) directions. At frequencies above 800 Hz the strongest responses were evoked by stimuli from the ipsilateral direction while gradually weaker responses were seen as the sound direction shifted towards the contralateral side. At frequencies between 500 and 800 Hz both directional patterns were seen. The directionality was highly intensity dependent. No special adaptations for localization of conspecific calls were found. Accepted: 23 November 1996     

Responses of the infrared sensilla of Melanophila acuminata (Coleoptera: Buprestidae) to monochromatic infrared stimulation

The pit organs of the beetle Melanophilaacuminata were stimulated with monochromatic infrared radiation using a continuous wave CO overtone infrared laser. Best sensitivity was in the wavelength range 2.8–3.5 μm. In this range a stimulus intensity of 14.7 mW cm⁻² was sufficient to generate single action potentials. At a wavelength of 5 μm receptor performance significantly decreased. An increase in stimulus intensity caused a decrease in response latency and an increase in the number of action potentials elicited. At a given wavelength (3.4 μm) the dynamic amplitude range of action potential responses covered 12 dB. At high stimulus intensities (94.2 mW cm⁻²) a stimulus duration of 4 ms was sufficient to generate one to two action potentials and a stimulus duration of 60 ms already caused response saturation (with up to nine action potentials). In a repetitive stimulus regime distinct receptor potentials were visible up to a frequency of 600 Hz. Accepted: 18 March 2000     

Relevance of nonlinear lumped-parameter models in the analysis of depth-EEG epileptic signals

In the field of epilepsy, the analysis of stereoelectroencephalographic (SEEG, intra-cerebral recording) signals with signal processing methods can help to better identify the epileptogenic zone, the area of the brain responsible for triggering seizures, and to better understand its organization. In order to evaluate these methods and to physiologically interpret the results they provide, we developed a model able to produce EEG signals from “organized” networks of neural populations. Starting from a neurophysiologically relevant model initially proposed by Lopes Da Silva et al. [Lopes da Silva FH, Hoek A, Smith H, Zetterberg LH (1974) Kybernetic 15: 27–37] and recently re-designed by Jansen et al. [Jansen BH, Zouridakis G, Brandt ME (1993) Biol Cybern 68: 275–283] the present study demonstrates that this model can be extended to generate spontaneous EEG signals from multiple coupled neural populations. Model parameters related to excitation, inhibition and coupling are then altered to produce epileptiform EEG signals. Results show that the qualitative behavior of the model is realistic; simulated signals resemble those recorded from different brain structures for both interictal and ictal activities. Possible exploitation of simulations in signal processing is illustrated through one example; statistical couplings between both simulated signals and real SEEG signals are estimated using nonlinear regression. Results are compared and show that, through the model, real SEEG signals can be interpreted with the aid of signal processing methods. Received: 3 January 2000 / Accepted: 24 March 2000     

Formation of the Vilsmeier-Haack complex: the performance of different levels of theory

Because of discrepancies in the available experimental data, an extensive theoretical investigation of the formation of the Vilsmeier-Haack (VH) complex has been carried out. The barriers to complex formation calculated using eight different density functional methods (BLYP, B2-PLYP, B3LYP, B3PW91, MPW1K, M06-2X, and PBE1PBE), MP2, and extrapolation techniques (CBS-QB3, G3B3) with several basis sets (6 − 31 + G**, 6 − 311++G**, 6 − 311 + (3df,2p), aug-cc-pVDZ, and aug-cc-pVTZ) were compared with experimental data. For the overall reaction, MP2/aug-cc-pVDZ and M06-2X/6−31 + G(d,p) perform best compared to the CBS techniques. The results help clarify some open mechanistic questions.     

A comparative assessment of four methods for estimating ammonia emissions at microclimatic locations in a dairy building

Ammonia emissions were estimated at five microclimatic locations in a free stall dairy building using four different methods. Measurements were performed simultaneously with the different methods to enable comparison. In the first method, the rate of ammonia emission from manure was theoretically modeled utilizing Fick’s law and boundary layer theory. In the second method, recirculation flux-chamber technique was used to model ammonia emission from manure. In the third and fourth methods, respectively, carbon dioxide and methane balances were employed to calculate ammonia emission. The mean ammonia emissions measured from the five locations using the different methods ranged from 0.10 to 0.15 g m⁻² h⁻¹. The percentage of variation of ammonia emission from the different location ranged between 8 and 52% for the different methods. Recorded ammonia emission rates in the dairy building were from 0.04 to 0.25 g m⁻² h⁻¹. The percentage of variation in ammonia, carbon dioxide, methane, and manure properties in the building was 50%. Two-way statistical analysis of variance showed that there were no significant differences (p > 0.63) between the four different methods or between the measurements obtained at the five locations (p > 0.90).     

Genetic stability of wood density and diameter in <Emphasis Type="Italic">Pinus radiata</Emphasis> D. Don plantation estate across Australia

Genetic variation for wood quality traits and diameter growth for radiata pine (Pinus radiata D. Don) at age 20/21 years was estimated from eight trials in Australia. The traits studied were wood density, acoustic time-of-flight (an indirect measure of stiffness) and diameter at breast height (DBH). Wood density and DBH exhibited significant additive genetic variation whereas non-additive effects were not significantly different from zero. Time of flight was also not significantly different from zero for both additive and non-additive effects, respectively. Average single-site heritability estimates (±SE) for wood density and DBH were 0.38 ± 0.10 and 0.16 ± 0.08, respectively. Pooled-site heritability estimates for wood density and DBH were 0.38 ± 0.10 and 0.08 ± 0.10, respectively. For density, there was little evidence of genotype-by-environment interaction (GEI) across the eight trials at the additive level (type B additive genetic correlation; r _BADD = 0.73 ± 0.08) and type B genetic correlation for full-sib families (r _BFS = 0.64 ± 0.08). In contrast, the type B additive genetic correlation for DBH was lower, (r _BADD = 0.51 ± 0.14), suggesting evidence of GEI. However, type B genetic correlation for full-sib families was moderate (0.63 ± 0.11) for DBH, suggesting that there may be some stable full-sib families. On the basis of the results of this study, GEI should be considered in order to optimise deployment of improved germplasm in Australia.     

Variability of the electric organ discharge interval duration in resting Gymnotus carapo

 We recorded the electric organ discharges of resting Gymnotus carapo specimens. We analyzed the time series formed by the sequence of interdischarge intervals. Nonlinear prediction, false nearest neighbor analyses, and comparison between the performance of nonlinear and linear autoregressive models fitted to the data indicated that nonlinear correlations between intervals were absent, or were present to a minor extent only. Following these analyses, we showed that linear autoregressive models with combined Gaussian and shot noise reproduced the variability and correlations of the resting discharge pattern. We discuss the implications of our findings for the mechanisms underlying the timing of electric organ discharge generation. We also argue that autoregressive models can be used to evaluate the changes arising during a wide variety of behaviors, such as the modification in the discharge intervals during interaction between fish pairs. Received: 14 March 2000 / Accepted in revised form: 9 October 2000     

Directed cortical information flow during human object recognition: analyzing induced EEG gamma-band responses in brain's source space

The increase of induced gamma-band responses (iGBRs; oscillations >30 Hz) elicited by familiar (meaningful) objects is well established in electroencephalogram (EEG) research. This frequency-specific change at distinct locations is thought to indicate the dynamic formation of local neuronal assemblies during the activation of cortical object representations. As analytically power increase is just a property of a single location, phase-synchrony was introduced to investigate the formation of large-scale networks between spatially distant brain sites. However, classical phase-synchrony reveals symmetric, pair-wise correlations and is not suited to uncover the directionality of interactions. Here, we investigated the neural mechanism of visual object processing by means of directional coupling analysis going beyond recording sites, but rather assessing the directionality of oscillatory interactions between brain areas directly. This study is the first to identify the directionality of oscillatory brain interactions in source space during human object recognition and suggests that familiar, but not unfamiliar, objects engage widespread reciprocal information flow. Directionality of cortical information-flow was calculated based upon an established Granger-Causality coupling-measure (partial-directed coherence; PDC) using autoregressive modeling. To enable comparison with previous coupling studies lacking directional information, phase-locking analysis was applied, using wavelet-based signal decompositions. Both, autoregressive modeling and wavelet analysis, revealed an augmentation of iGBRs during the presentation of familiar objects relative to unfamiliar controls, which was localized to inferior-temporal, superior-parietal and frontal brain areas by means of distributed source reconstruction. The multivariate analysis of PDC evaluated each possible direction of brain interaction and revealed widespread reciprocal information-transfer during familiar object processing. In contrast, unfamiliar objects entailed a sparse number of only unidirectional connections converging to parietal areas. Considering the directionality of brain interactions, the current results might indicate that successful activation of object representations is realized through reciprocal (feed-forward and feed-backward) information-transfer of oscillatory connections between distant, functionally specific brain areas.     

Advanced backcross-QTL analysis in spring barley (H. vulgare ssp. spontaneum) comparing a REML versus a Bayesian model in multi-environmental field trials

A common difficulty in mapping quantitative trait loci (QTLs) is that QTL effects may show environment specificity and thus differ across environments. Furthermore, quantitative traits are likely to be influenced by multiple QTLs or genes having different effect sizes. There is currently a need for efficient mapping strategies to account for both multiple QTLs and marker-by-environment interactions. Thus, the objective of our study was to develop a Bayesian multi-locus multi-environmental method of QTL analysis. This strategy is compared to (1) Bayesian multi-locus mapping, where each environment is analysed separately, (2) Restricted Maximum Likelihood (REML) single-locus method using a mixed hierarchical model, and (3) REML forward selection applying a mixed hierarchical model. For this study, we used data on multi-environmental field trials of 301 BC₂DH lines derived from a cross between the spring barley elite cultivar Scarlett and the wild donor ISR42-8 from Israel. The lines were genotyped by 98 SSR markers and measured for the agronomic traits “ears per m2,” “days until heading,” “plant height,” “thousand grain weight,” and “grain yield”. Additionally, a simulation study was performed to verify the QTL results obtained in the spring barley population. In general, the results of Bayesian QTL mapping are in accordance with REML methods. In this study, Bayesian multi-locus multi-environmental analysis is a valuable method that is particularly suitable if lines are cultivated in multi-environmental field trials. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Nonlinear EEG analysis based on a neural mass model

The well-known neural mass model described by Lopes da Silva et al. (1976) and Zetterberg et al. (1978) is fitted to actual EEG data. This is achieved by reformulating the original set of integral equations as a continuous-discrete state space model. The local linearization approach is then used to discretize the state equation and to construct a nonlinear Kalman filter. On this basis, a maximum likelihood procedure is used for estimating the model parameters for several EEG recordings. The analysis of the noise-free differential equations of the estimated models suggests that there are two different types of alpha rhythms: those with a point attractor and others with a limit cycle attractor. These attractors are also found by means of a nonlinear time series analysis of the EEG recordings. We conclude that the Hopf bifurcation described by Zetterberg et al. (1978) is present in actual brain dynamics. Received: 11 August 1997 / Accepted in revised form: 20 April 1999     

In silico QSAR studies of anilinoquinolines as EGFR inhibitors

Members of the epidermal growth factor receptor (EGFR) family of proteins are frequently overactive in solid tumors. A relatively new therapeutic approach to inhibit the kinase activity is the use of ATP-competitive small molecules. In silico techniques were employed to identify the key interactions between inhibitors and their protein receptors. A series of EGFR inhibitory anilinoquinolines was studied within the framework of hologram quantitative structure activity relationship (HQSAR), density functional theory (DFT)-based QSAR, and three-dimensional (3D) QSAR (CoMFA/CoMSIA). The HQSAR analysis implied that substitutions at certain sites on the inhibitors play an important role in EGFR inhibition. DFT-based QSAR results suggested that steric and electronic interactions contributed significantly to the activity. Ligand-based 3D-QSAR and receptor-guided 3D-QSAR analyses such as CoMFA and CoMSIA techniques were carried out, and the results corroborated the previous two approaches. The 3D QSAR models indicated that steric and hydrophobic interactions are dominant, and that substitution patterns are an important factor in determining activity. Molecular docking was helpful in identifying a bioactive conformer as well as a plausible binding mode. The docked geometry-based CoMFA model with steric and electrostatic fields effect gave q ² = 0.66, r ² = = 0.94 with r ² _predictive = 0.72. Similarly, CoMSIA with hydrophobic field gave q ² = 0.59, r ² = 0.85 with r ² _predictive = 0.63. Bulky groups around site 3 of ring “C”, and hydrophilic and bulky groups at position 6 of ring “A” are desirable, with a hydrophobic and electron-donating group at site 7 of ring “A” being helpful. Accordingly, potential EGFR inhibitors may be designed by modification of known inhibitors.