A natural communication system on genome evolution

正The central dogma of molecular biology describes the flow of genetic information from DNA via RNA to protein and duplication from ancestral to descendent DNA(Crick,1958).However,the genetic information could not be quantified and mathematically modeled.So it differs from theinformationformulated by Shannon and used in information and coding theories(Shannon,1949).Although physicists have suggested that life absorbs negative entropy(or information)from the environment(Schrodinger et al.,1944),no physical     

Different aspects of bacterial communication signals

The communication or quorum-sensing signal molecules (QSSM) are specialized molecules used by numerous gram-negative bacterial pathogens of animals and plants to regulate or modulate bacterial virulence factor production. In plant-associated bacteria, genes encoding the production of these signal molecules, QSSMs, were discovered to be linked with the phenotype of bacterium, because mutation of these genes typically disrupts some behaviors of bacteria. There are other regulator genes which respond to the presence of signal molecule and regulate the production of signal molecule as well as some virulence factors. The synthesis and regulator genes (collectively called quorum-sensing genes hereafter) are repressed in low bacterial population but induced when bacteria reach to high cell density. Multiple regulatory components have been identified in the bacteria that are under control of quorum sensing. This review describes different communication signal molecules, and the various chemical, physical and genomic factors known to synthesize signals. Likewise, the role of some signal-degrading enzymes or compounds and the interaction of QSSMs with eukaryotic metabolism will be discussed here.     

Frameshift signals in genes associated with the circular code

Three sets of 20 trinucleotides are preferentially associated with the reading frames and their 2 shifted frames of both eukaryotic and prokaryotic genes. These 3 sets are circular codes. They allow retrieval of any frame in genes (containing these circular code words), locally anywhere in the 3 frames and in particular without start codons in the reading frame, and automatically with the reading of a few nucleotides. The circular code in the reading frame, noted X, which can deduce the 2 other circular codes in the shifted frames by permutation, is the information used for analysing frameshift genes, i. e. genes with a change of reading frame during translation. This work studies the circular code signal around their frameshift sites. Two scoring methods are developed, a function P based on this code X and a function Q based both on this code X and the 4 trinucleotides with identical nucleotides. They detect a significant correlation between the code X and the -1 frameshift signals in both eukaryotic and prokaryotic genes, and the +1 frameshift signals in eukaryotic genes.     

A method for computerized modification of certain natural animal sounds for communication study purposes

A new method for computerized modification of sound signals is presented. With digital signal processing in the time domain it is possible to alter the amplitude, the frequency and the time scale of natural sounds independently. The method can be applied to natural sounds with reasonably pure tonal quality.     

The natural variation of a neural code

The way information is represented by sequences of action potentials of spiking neurons is determined by the input each neuron receives, but also by its biophysics, and the specifics of the circuit in which it is embedded. Even the "code" of identified neurons can vary considerably from individual to individual. Here we compared the neural codes of the identified H1 neuron in the visual systems of two families of flies, blow flies and flesh flies, and explored the effect of the sensory environment that the flies were exposed to during development on the H1 code. We found that the two families differed considerably in the temporal structure of the code, its content and energetic efficiency, as well as the temporal delay of neural response. The differences in the environmental conditions during the flies' development had no significant effect. Our results may thus reflect an instance of a family-specific design of the neural code. They may also suggest that individual variability in information processing by this specific neuron, in terms of both form and content, is regulated genetically.     

Chromosome- and spindle-pole-derived signals generate an intrinsic code for spindle position and orientation

Mitotic spindle positioning by cortical pulling forces defines the cell division axis and location, which is critical for proper cell division and development. Although recent work has identified developmental and extrinsic cues that regulate spindle orientation, the contribution of intrinsic signals to spindle positioning and orientation remains unclear. Here, we demonstrate that cortical force generation in human cells is controlled by distinct spindle-pole- and chromosome-derived signals that regulate cytoplasmic dynein localization. First, dynein exhibits a dynamic asymmetric cortical localization that is negatively regulated by spindle-pole proximity, resulting in spindle oscillations to centre the spindle within the cell. We find that this signal comprises the spindle-pole-localized polo-like kinase (Plk1), which regulates dynein localization by controlling the interaction between dynein-dynactin and its upstream cortical targeting factors NuMA and LGN. Second, a chromosome-derived RanGTP gradient restricts the localization of NuMA-LGN to the lateral cell cortex to define and maintain the spindle orientation axis. RanGTP acts in part through the nuclear localization sequence of NuMA to locally alter the ability of NuMA-LGN to associate with the cell cortex in the vicinity of chromosomes. We propose that these chromosome- and spindle-pole-derived gradients generate an intrinsic code to control spindle position and orientation.     

Oxylipins as developmental and host-fungal communication signals

Pathogenic microbes and their hosts have acquired complex signalling mechanisms to appraise themselves of the environmental milieu in the ongoing battle for survival. Several recent studies have implicated oxylipins as a novel class of host-microbe signalling molecules. Oxylipins represent a vast and diverse family of secondary metabolites that originate from the oxidation or further conversion of polyunsaturated fatty acids. Among the microbial oxylipins, the fungal oxylipins are best characterized and function as hormone-like signals that modulate the timing and balance between asexual and sexual spore development in addition to toxin production. Coupled with other studies that implicate a role for fungal oxylipins in pathogenesis by Aspergillus and Candida spp., these results suggest that host and microbial oxylipins might interfere with the metabolism, perception or signalling processes of each other.     

Silent communication: toward using brain signals

From the 1980s movie Firefox to the more recent Avatar, popular science fiction has speculated about the possibility of a persons thoughts being read directly from his or her brain. Such braincomputer interfaces (BCIs) might allow people who are paralyzed to communicate with and control their environment, and there might also be applications in military situations wherever silent user-to-user communication is desirable. Previous studies have shown that BCI systems can use brain signals related to movements and movement imagery or attention-based character selection. Although these systems have successfully demonstrated the possibility to control devices using brain function, directly inferring which word a person intends to communicate has been elusive. A BCI using imagined speech might provide such a practical, intuitive device. Toward this goal, our studies to date addressed two scientific questions: (1) Can brain signals accurately characterize different aspects of speech? (2) Is it possible to predict spoken or imagined words or their components using brain signals?     

Analysis of temporal patterns of communication signals

Temporal pattern is a crucial feature of communication signals, and neurons in the brains of many animals respond selectively to behaviorally relevant temporal features of sensory stimuli. Many aspects of neural function contribute to this selectivity, including membrane biophysics, channel properties, synaptic physiology and network structure.     

Issues in the classification of multimodal communication signals

Communication involves complex behavior in multiple sensory channels, or "modalities." We provide an overview of multimodal communication and its costs and benefits, place examples of signals and displays from an array of taxa, sensory systems, and functions into our signal classification system, and consider issues surrounding the categorization of multimodal signals. The broadest level of classification is between signals with redundant and nonredundant components, with finer distinctions in each category. We recommend that researchers gather information on responses to each component of a multimodal signal as well as the response to the signal as a whole. We discuss the choice of categories, whether to categorize signals on the basis of the signal or the response, and how to classify signals if data are missing. The choice of behavioral assay may influence the outcome, as may the context of the communicative event. We also consider similarities and differences between multimodal and unimodal composite signals and signals that are sequentially, rather than simultaneously, multimodal.     

Pursuit-deterrent signals: communication between prey and predator

When encountering predators, prey animals often expose themselves by loud vocalization, by repeated movements or by revealing conspicuous colors. The more elaborate displays were often considered to be warning signals directed to other prey, and the less obvious displays to be intention movements. During the last decade, there has been increasing evidence that, in fact, prey display is aimed at the predator, apparently to deter further pursuit. This communication between two seemingly unlikely partners, prey and predator, appears to be based upon a common interest - satisfying the predator's need for further information.     

Sickness-related odor communication signals as determinants of social behavior in rat: A role for inflammatory processes

Infected animals are avoided by conspecifics, suggesting that the inflammatory cascade may play a significant role in odor communication. Injection of male rats with the bacterial mimetic, lipopolysaccharide (LPS, 100 μg/kg, i.p.), decreased investigation through a wire-mesh partition between healthy male partners. This avoidance response was observed in adult males in response to soiled bedding collected from sick rats, regardless of whether LPS was injected peripherally (100 μg/kg, i.p.) or centrally (0.25 or 2.5 μg, icv). The release of sickness-related odor cues was dose-dependently blocked by icv infusion of the anti-inflammatory cytokine, interleukin-10 (IL-10; 20 or 200 ng), and reproduced by icv infusion of pro-inflammatory cytokine, IL-1β (5 or 50 ng). Subcutaneous pretreatment with either estradiol benzoate (20 μg/kg) or testosterone propionate (50 or 500 μg/kg) to adult males that were administered LPS inhibited release of aversive odor cues, but these hormones alone did not influence odor properties. Importantly, the avoidance response to sickness-related odor was not associated with changes in plasma corticosterone, testosterone, or IL-6 levels of odor donors. However, plasma IL-1β concentrations of sick animals was in fact predictive of aversive responses in conspecifics, suggesting that the inflammatory cascade, but not plasma steroid hormones, is likely to mediate aversive properties in odor that functions to signal illness state to conspecifics.     

A ratio code for vibrotactile pitch

Subjective impressions of pitch for 80 different sinusoidal vibrotactile stimuli delivered to the index finger were measured by free magnitude estimation in four subjects. In three of the subjects, pitch at a given frequency decreased as stimulus amplitude increased. The data of these subjects were well described by a model of pitch based on the relative levels of activation of the three major tactile channels. The main element in this model was a ratio of P channel activity to the sum of the activity levels of the P, NPI, and NPIII channels. Activity levels of the channels were estimated on the basis of the psychophysical literature, including a study of vibrotactile loudness using the same subjects and stimuli as those employed here. A fourth subject, whose pattern of loudness judgments had previously been shown to differ from those of the other subjects, did not conform to this pitch model: her data revealed significant increases in pitch with increases in amplitude, and appear to reflect an inability to combine signals across vibrotactile channels. Pitch changes resulting from vibrotactile adaptation were directionally consistent with our ratio model: pitch was slightly increased by adaptation to a 25 Hz stimulus, and slightly decreased by 200 Hz adaptation.     

Temporal population code of concurrent vocal signals in the auditory midbrain

Unique patterns of spike activity across neuron populations have been implicated in the coding of complex sensory stimuli. Delineating the patterns of neural activity in response to varying stimulus parameters and their relationships to the tuning characteristics of individual neurons is essential to ascertaining the nature of population coding within the brain. Here, we address these points in the midbrain coding of concurrent vocal signals of a sound-producing fish, the plainfin midshipman. Midshipman produce multiharmonic vocalizations which frequently overlap to produce beats. We used multivariate statistical analysis from single-unit recordings across multiple animals to assess the presence of a temporal population code. Our results show that distinct patterns of temporal activity emerge among midbrain neurons in response to concurrent signals that vary in their difference frequency. These patterns can serve to code beat difference frequencies. The patterns directly result from the differential temporal coding of difference frequency by individual neurons. Difference frequency encoding, based on temporal patterns of activity, could permit the segregation of concurrent vocal signals on time scales shorter than codes requiring averaging. Given the ubiquity across vertebrates of auditory midbrain tuning to the temporal structure of acoustic signals, a similar temporal population code is likely present in other species.