Long-term changes in a benthic assemblage associated with artificial reefs

The aim of the study was to evaluate the long-term development of a hard bottom benthic assemblage over a period of 20 years in an area off the mouth of a large river. The artificial reef of Fregene was selected because benthic assemblage data were available for the period 1981–1992. This artificial reef is located in the mid Tyrrhenian Sea, 5 nautical miles north of the two mouths of the Tevere River (Latium, Italy) and 1.5 nautical miles offshore from Fregene (Rome, Italy). The artificial reef was deployed in March 1981 for fisheries enhancement in 10–14 m of water on a sandy-silty seabed. The Tevere River carries suspended materials and a heavy load of organics since it transports Rome’s effluent, resulting in the eutrophic state of area waters. Benthic sampling was conducted in 2001 by SCUBA diving; two standard surfaces of 400 cm² were scraped from the vertical walls of the same uppermost block in four different periods. All organisms were identified and counted. The methodology used is the same as that adopted in the previous periods, so that the 2001 data could be compared with past collected data. The benthic assemblage was analysed by cluster analysis using the Bray-Curtis index and clustered using the group average clustering algorithm. The SIMPER procedure was used to identify those taxa that characterize each station group identified by cluster analysis. Changes in benthic assemblages and hydrological trends of the Tevere River were investigated using the cumulative sum series method. The 20-year development of the benthic community, starting from the new substratum, is composed of different phases characterised by different benthic assemblages. In particular five different phases were distinguished: 1. Pioneer species recruitment (May 1981–June 1981); 2. Mytilus galloprovincialis (mussel) dominance (August 1981–November 1983); 3. M. galloprovincialis regression (July 1984–October 1985); 4. M. galloprovincialis absence (91–92); 5. Bryozoans bioconstruction dominance (2001). The dynamic succession of the observed benthic assemblages exhibited a good relation with the Tevere River flow. The Tevere River flow, and the subsequent sedimentation process, seems to have strongly influenced the benthic assemblage succession of the Fregene artificial reef. Guest editors: G. Relini & J. Ryland Biodiversity in Enclosed Seas and Artificial Marine Habitats     

The intra-annual variability of soft-bottom macrobenthos abundance patterns in the North Channel of the Seine estuary

Temporal and spatial variability of the Abra alba–Pectinaria koreni and Macoma balthica communities was examined in the northern part of the Seine estuary (North Channel) over different space and time scales in order to assess the role that the hydrologic regime and/or anthropogenic influences play in defining benthic communities over time. Sediment in the North Channel displayed strong spatial and temporal variability, sustained by intense sediment transport episodes. Total macrobenthic abundances ranged widely on the course of the year and there was no evidence of a seasonal signal for the density fluctuations, whatever the spatial scale considered. The bio-sedimentary dynamics can be divided into two periods: the first corresponds to the high flow rate period (January–May) during which fauna is influenced by fine silt/clay deposition, and the second to the low flow rate period (June–December) during which sandy deposits prevail. Despite the absence of significant correlations between sediment composition and abundance, episodes of sediment transport seem to be an important structuring mechanism in the Seine estuary. As a consequence, the faunal composition varied throughout the year. The winter and spring fauna, characterised by species living on muddy fine-sands or muds, were enriched during the summer and autumn by species living in clean fine sand, such as Donax vittatus, Nephtys cirrosa or Spio decoratus, mainly represented by adult individuals. Secondary settlement of drifters may explain the rapid structuration of assemblages a few days after the sandy deposits. Our results suggest the importance of the bentho-pelagic coupling, primarily induced by the sedimentary instability, on the macrobenthic fauna dynamics. The intra-annual variability of assemblages at the mouth of the Seine river and the silted situation of the North Channel might simply be the result of the silting up and alteration of the inner estuary, generated by several decades of man-made modifications and natural processes.     

Efficient inhibition of bursts by bursts in the auditory system of crickets

In crickets, auditory information about ultrasound is carried bilaterally to the brain by the AN2 neurons. The ON1 neuron provides contralateral inhibitory input to AN2, thereby enhancing bilateral contrast between the left and right AN2s, an important cue for sound localization. We examine how the structures of the spike trains of these neurons affect this inhibitory interaction. As previously shown for AN2, ON1 responds to salient peaks in stimulus amplitude with bursts of spikes. Spike bursts, but not isolated spikes, reliably signal the occurrence of specific features of the stimulus. ON1 and AN2 burst at similar times relative to the amplitude envelope of the stimulus, and bursts are more tightly time-locked to stimulus feature than the isolated spikes. As a consequence, spikes that, in the absence of contralateral inhibition, would occur within AN2 bursts are more likely to be preceded by spikes in ON1 (mainly also in bursts) than are isolated AN2 spikes. This leads to a large decrease in the burst rate of the inhibited AN2. We conclude that the match in coding properties of ON1 and AN2 allows contralateral inhibition to be most efficient for those portions of the response that carry the behaviourally relevant information, i.e. for bursts. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

海豚的神经系统是如何利用声波定方向的？

海豚和蝙蝠等神经系统利用两耳效应来检测声音的方向,这为大家所熟知,海豚和蝙蝠要靠听觉代替视觉来捕食和躲避敌人,用双耳快速测定声源的方向,神经系统如何能达到这一目的？在数字技术中求两个波形相位差有一套复杂的算法。可是经这篇文章的分析,在神经系统中处理相位差却出奇地简单,它只需一个神经元就可完成计算。这为我们进一步认识神经系统信息处理机理提供了一个例证。经计算机仿真证明它具有很多特别的优点。也为信息处理技术提供了一个新的方法。     

在系统发育分析中编码空位

空位包含了可用于系统发育分析的进化信息.为了准确地计算系统发育关系,空位包含的信息应该予以考虑.本文讨论了7种最常用的空位编码方法,并举例说明这些方法的编码原理.另外,本文还介绍了一些经验用以帮助研究者在使用现有的系统发育软件时选择空位编码方法.但是,所有的空位编码方法都有其优点和缺点,需要提出新的空位编码方法才能使空位信息在系统发育分析中得以充分地应用.     

Application of the secondary structure model of rRNA for phylogeny: D2-D3 expansion segments of the LSU gene of plant-parasitic nematodes from the family Hoplolaimidae Filipjev, 1934

Knowledge of rRNA structure is increasingly important to assist phylogenetic analysis through reconstructing optimal alignment, utilizing molecule features as an additional source of data and refining appropriate models of evolution of the molecule. We describe a procedure of optimization for alignment and a new coding method for nucleotide sequence data using secondary structure models of the D2 and D3 expansion fragments of the LSU-rRNA gene reconstructed for fifteen nematode species of the agriculturally important and diverse family Hoplolaimidae, order Tylenchida. Using secondary structure information we converted the original sequence data into twenty-eight symbol codes and submitted the transformed data to maximum parsimony analysis. We also applied the original sequence data set for Bayesian inference. This used the doublet model with sixteen states of nucleotide doublets for the stem region and the standard model of DNA substitution with four nucleotide states for loops and bulges. By this approach, we demonstrate that using structural information for phylogenetic analyses led to trees with lower resolved relationships between clades and likely eliminated some artefactual support for misinterpreted relationships, such as paraphyly of Helicotylenchus or Rotylenchus. This study as well as future phylogenetic analyses is herein supported by the development of an on-line database, NEMrRNA, for rRNA molecules in a structural format for nematodes. We also have developed a new computer program, RNAstat, for calculation of nucleotide statistics designed and proposed for phylogenetic studies.     

Genomic noncoding sequences and the size of eukaryotic cell nucleus as important factors of gene protection from chemical mutagens

An improved quantitative model describing a protective function of eukaryotic genomic noncoding sequences was developed. In this new model, two factors affecting gene protection from chemical mutagensare considered: (1) the ratio of the total lengths of coding and noncoding genomic sequences and (2) the volume of the cell nucleus. An increase in the noncoding DNA in the genome reduces the number of mutagen-damaged nucleotides in the coding region, whereas an increase in the volume of the nucleus decreases the flow of mutagens per unit of nuclear volume that attacks its surface.     

The role of temporal generalization in a temporal discrimination task

Two experiments trained rats to discriminate two or three stimulus durations using a temporal discrimination task. A standard peak shift effect was observed when training was administered with short versus long signals in Experiment 1. Both discrimination accuracy scores and the generalization gradients revealed that shorter intervals were discriminated more accurately, which may be due to the scalar property of timing. In Experiment 2, three signals (short, medium, and long) were associated with three different responses, or two of the intervals were associated with one response (short and long or short and medium) and the other interval with a different response. Here, the short/medium versus long discrimination was learned most readily of the three tasks. The results of both experiments indicated a strong contribution of learning of individual durations combined with scalar generalization gradients, but Experiment 2 indicated that categorical encoding of durations may have also been operating.     

Shifts in the psychophysical function in rats

The primary goal was to compare results from a free-operant procedure with pigeons [Machado, A., Guilhardi, P., 2000. Shifts in the psychometric function and their implications for models of timing. J. Exp. Anal. Behav. 74, 25-54, Experiment 2] with new results obtained with rats. The secondary goal was to compare the results of both experiments with dependent variables that were not used in the original publication. As in the original study with pigeons, rats were trained on a two-alternative free-operant psychophysical procedure in which left lever press responses were reinforced during the first and second quarters of a 60-s trial, and right lever press responses were reinforced during the third and fourth quarters of the trial. The quarters were reinforced according to four independent variable interval (VI) schedules of reinforcement. The VI duration was manipulated in each quarter, and shifts in the psychophysical functions that relate response rate with time since trial onset were measured. The results obtained with rats were consistent with those previously obtained with pigeons. In addition, results not originally reported were also consistent between rats and pigeons, and provided insights into the perception, memory, and decision processes in Scalar Expectancy Theory and Learning-to-Time Theory.     

Temporal generalization accounts for response resurgence in the peak procedure

The peak interval (PI) procedure is commonly used to evaluate animals' ability to produce timed intervals. It consists of presenting fixed interval (FI) schedules in which some of the trials are replaced by extended non-reinforced trials. Responding will often resume (resurge) at the end of the non-reinforced trials unless precautions are taken to prevent it. Response resurgence was replicated in rats and pigeons. Variation of the durations of the FI and the non-reinforced probe trials showed it to be dependent on the time when reinforcement is expected. Timing of both the normal time to reinforcement, and the subsequent time to reinforcement during the probe trials followed Weber's law. A quantitative model of resurgence is described, suggesting how animals respond to the signaling properties of reinforcement omission. Model results were simulated using a stochastic binary counter.