Demarcated response sequences and generalised matching

The generalised matching law was applied for the first time to sequences of responses. Pigeons responded on dependently arranged two-operandum concurrent schedules in which all four possible two-response sequences on these operanda were demarcated and reinforced. Reinforcer rates for the sequences were varied over a wide range, including extinction. Sequences of responses, rather than individual responses, followed the generalised matching law. We compared single-sensitivity and multiple-sensitivity versions of the generalised matching law. The multiple sensitivities were not significantly different from each other, so the single-sensitivity model provided the more efficient fit. As in previous research, responding was biased against the emission of sequences that required changeovers.     

A lexical approach for identifying behavioural action sequences

Animals display characteristic behavioural patterns when performing a task, such as the spiraling of a soaring bird or the surge-and-cast of a male moth searching for a female. Identifying such recurring sequences occurring rarely in noisy behavioural data is key to understanding the behavioural response to a distributed stimulus in unrestrained animals. Existing models seek to describe the dynamics of behaviour or segment individual locomotor episodes rather than to identify the rare and transient sequences of locomotor episodes that make up the behavioural response. To fill this gap, we develop a lexical, hierarchical model of behaviour. We designed an unsupervised algorithm called “BASS” to efficiently identify and segment recurring behavioural action sequences transiently occurring in long behavioural recordings. When applied to navigating larval zebrafish, BASS extracts a dictionary of remarkably long, non-Markovian sequences consisting of repeats and mixtures of slow forward and turn bouts. Applied to a novel chemotaxis assay, BASS uncovers chemotactic strategies deployed by zebrafish to avoid aversive cues consisting of sequences of fast large-angle turns and burst swims. In a simulated dataset of soaring gliders climbing thermals, BASS finds the spiraling patterns characteristic of soaring behaviour. In both cases, BASS succeeds in identifying rare action sequences in the behaviour deployed by freely moving animals. BASS can be easily incorporated into the pipelines of existing behavioural analyses across diverse species, and even more broadly used as a generic algorithm for pattern recognition in low-dimensional sequential data.     

我国肾综合征出血热疫苗生产株LR1株的全基因组序列分析

为测定我国肾综合征出血热疫苗生产株LR1株的全基因组序列 ,了解该株分子基础 ,从提取的细胞总RNA逆转录PCR扩增 ,产物纯化后克隆T载体纯化后测序 ,结果证明 ,LR1株全基因组序列由L6 5 33、M36 16、S片段的16 92个核苷酸组成 ,依各自读码框架分别编码 2 15 1、1135、42 9个氨基酸。序列同源比较分析表明 ,LR1毒株与国外HTN型毒株高度同源 ,属同一亚型 ,尤其与HTN代表株 76 - 1183个片段同源率高达 99 3%～ 99 8% ,而与国内的HTN型病毒差异较大 ,同源率仅为 79 4%～ 84 6 %。氨基酸比较也显示了同样的结果。     

Basal ganglia neural mechanisms of natural movement sequences

Natural rodent grooming and other instinctive behavior serves as a natural model of complex movement sequences. Rodent grooming has syntactic (rule-driven) sequences and more random movement patterns. Both incorporate the same movements--only the serial structure differs. Recordings of neural activity in the dorsolateral striatum and the substantia nigra pars reticulata indicate preferential activation during syntactic sequences over more random sequences. Neurons that are responsive during syntactic grooming sequences are often unresponsive or have reverse activation profiles during kinematically similar movements that occur in flexible or random grooming sequences. Few neurons could be categorized as strictly movement related--instead they were activated only in the context of particular sequential patterns of movements. Particular sequential patterns included "syntactic chain" grooming sequences of paw, head, and body movements and also "warm-up" sequences, which consist of head and body/limb movements that precede locomotion after a period of quiet resting (Golani 1992). Activation during warm-up was less intense and less frequent than during grooming sequences, but both sequences activated neurons above baseline levels, and the same neurons sometimes responded to both sequences. The fact that striatal neurons code 2 natural sequences which are made up of different constituent movements suggests that the basal ganglia may have a generalized role in sequence control. The basal ganglia are modulated by the context of the sequence and may play an executive function in the complex natural patterns of sequenced behaviour.     

Sexual behaviour of Anastrepha obliqua (Macquart) (Diptera: Tephritidae): Do laboratory domestication conditions influence male courtship behaviour?

We analysed the influence of laboratory domestication, under relaxed conditions, on the courtship behaviour of the fruit fly species Anastrepha obliqua, an important agricultural pest. We compared the temporal patterns of pheromone emission (Calling behaviour) and the frequencies and sequences of the courtship behavioural units of males of a laboratory lineage and a wild lineage. Our results indicated similarities in the temporal behavioural patterns of calling, the durations of their behavioural sequences, the final sequences of courtships resulting in copulation, of wild and laboratory males. Differences, however, were observed between the two populations in terms of the frequencies of the behavioural units executed and the initial sequence of courtship. Differences were noted in the presence or absence of some behavioural units within the courtship behavioural repertoires of the laboratory-reared and wild. The wild males did not show units such as Alignment, Contact, Fighting and Marking Leaf that were observed in the laboratory males' courtship behaviour under laboratory conditions; on the other hand, laboratory males did not show the Abdominal movements and Oscillation observed in the courtship behaviour of wild males. The rearing of A. obliqua males under relaxed conditions in the laboratory provides an environment adequate for the preservation of behavioural characteristics relevant to the successful mating, such as Movement, Arrowhead 1, and Attempt, and in temporal patterns of pheromone emission.     

A Penalized Likelihood Approach for Bivariate Conditional Normal Models for Dynamic Co‐expression Analysis

Summary Gene co‐expressions have been widely used in the analysis of microarray gene expression data. However, the co‐expression patterns between two genes can be mediated by cellular states, as reflected by expression of other genes, single nucleotide polymorphisms, and activity of protein kinases. In this article, we introduce a bivariate conditional normal model for identifying the variables that can mediate the co‐expression patterns between two genes. Based on this model, we introduce a likelihood ratio (LR) test and a penalized likelihood procedure for identifying the mediators that affect gene co‐expression patterns. We propose an efficient computational algorithm based on iterative reweighted least squares and cyclic coordinate descent and have shown that when the tuning parameter in the penalized likelihood is appropriately selected, such a procedure has the oracle property in selecting the variables. We present simulation results to compare with existing methods and show that the LR‐based approach can perform similarly or better than the existing method of liquid association and the penalized likelihood procedure can be quite effective in selecting the mediators. We apply the proposed method to yeast gene expression data in order to identify the kinases or single nucleotide polymorphisms that mediate the co‐expression patterns between genes.     

String analysis and energy minimization in the partition of DNA sequences

Two approaches to the understanding of biological sequences are confronted. While the recognition of particular signals in sequences relies on complex physical interactions, the problem is often analysed in terms of the presence or absence of literal motifs (strings) in the sequence. We present here a test-case for evaluating the potential of this approach. We classify DNA sequences as positive or negative depending on whether they contain a single melted domain in the middle of the sequence, which is a global physical property. Two sets of positive "biological" sequences were generated by a computer simulation of evolutionary divergence along the branches of a phylogenetic tree, under the constraint that each intermediate sequence be positive. These two sets and a set of random positive sequences were subjected to pattern analysis. The observed local patterns were used to construct expert systems to discriminate positive from negative sequences. The experts achieved 79% to 90% success on random positive sequences and up to 99% on the biological sets, while making less than 2% errors on negative sequences. Thus, the global constraints imposed on sequences by a physical process may generate local patterns that are sufficient to predict, with a reasonable probability, the behaviour of the sequences. However, rather large sets of biological sequences are required to generate patterns free of illegitimate constraints. Furthermore, depending upon the initial sequence, the sets of sequences generated on a phylogenetic tree may be amenable or refractory to string analysis, while obeying identical physical constraints. Our study clarifies the relationship between experts' errors on positive and negative sequences, and the contributions of legitimate and illegitimate patterns to these errors. The test-case appears suitable both for further investigations of problems in the theory of sequence evolution and for further testing of pattern analysis techniques.     

Databases, models, and algorithms for functional genomics

A variety of patterns have been observed on the DNA and protein sequences that serve as control points for gene expression and cellular functions. Owing to the vital role of such patterns discovered on biological sequences, they are generally cataloged and maintained within internationally shared databases. Furthermore,the variability in a family of observed patterns is often represented using computational models in order to facilitate their search within an uncharacterized biological sequence. As the biological data is comprised of a mosaic of sequence-levels motifs, it is significant to unravel the synergies of macromolecular coordination utilized in cell-specific differential synthesis of proteins. This article provides an overview of the various pattern representation methodologies and the surveys the pattern databases available for use to the molecular biologists. Our aim is to describe the principles behind the computational modeling and analysis techniques utilized in bioinformatics research, with the objective of providing insight necessary to better understand and effectively utilize the available databases and analysis tools. We also provide a detailed review of DNA sequence level patterns responsible for structural conformations within the Scaffold or Matrix Attachment Regions (S/MARs).     

PERFORMANCE OF TADPOLES FROM THE HYBRIDOGENETIC RANA ESCULENTA COMPLEX: INTERACTIONS WITH POND DRYING AND INTERSPECIFIC COMPETITION

The performance of three genotypes (LL, LR, RR) of tadpoles resulting from the hybrid mating system of Rana lessonae (phenotype L, genotype LL) and Rana esculenta (phenotype E, genotype LR) was determined in artificial ponds. The effects of interspecific competition and pond drying on growth, development, and survival of tadpoles were used to measure the performance of genotypes and the relative fitness of offspring. Among the three genotypes, tadpoles from the homogametic mating RR had the lowest survival, growth, and development under all environmental conditions. Body size of the LL and LR genotype tadpoles at metamorphosis was reduced by competition and pond drying. Days to metamorphosis were also higher for the LL and LR genotype tadpoles in competition ponds. The proportion of individuals metamorphosing of each genotype was differentially lowered by competition and pond drying. The LL genotype produced more metamorphs than the LR genotype in the constant water level ponds, but the LR genotype produced more in drying ponds. In competition ponds, the LR genotype produced more metamorphs than the LL genotype, but the LL genotype produced more metamorphs in ponds without competition. The RR genotype produced no metamorphs in any of the experimental environments. Increased performance of LR offspring from the heterogametic mating, in harsh conditions, and reduced performance of RR offspring from the homogametic mating, even under favorable conditions, relative to the parental genotype (LL) suggests that the population dynamics of this hybridogenetic system is strongly dependent on mate choice in mixed populations and the subsequent pond environment females select for oviposition and larval development.     

Choosy females and indiscriminate males: mate choice in mixed populations of sexual and hybridogenetic water frogs (Rana lessonae, Rana esculenta)

For several decades, behavioral ecologists have studied theeffects of the environment on the behavior of individuals;but only fairly recently they have started to ask the reversequestion: how do the behavioral strategies of individuals affectthe composition and dynamics of populations and communities?Although intuitively obvious, this feedback from individualto higher levels is difficult to demonstrate, except in systemswith exceptionally fast and marked responses of the populationsto the behavior of its members. Such a system exists in sperm-dependentspecies. In European water frogs, for instance, successfulreproduction of a hybrid species (R. esculenta, genotype LR)requires mating with one of its parental species (R. lessonae,genotype LL), except in the rare cases where hybrids are triploid.The sexual host LL, however, should avoid matings with the sexual parasite LR, because the resulting LR offspring willeliminate the L genome from their germ line. In this studywe investigate how this conflict is solved. Since water froghybrids come in both sexes, rather than as females only likein other sperm-dependent systems, we performed the tests withboth females and males. One individual was given a choice betweentwo individuals of the opposite sex, one an LL and the otheran LR. In both species, females showed the predicted preferencefor LL males, whereas males did not discriminate between LLand LR females. On the individual level, we interpret the sexdifference in choosiness by the lower costs from mating withthe wrong species (LR) and the higher benefits from matingwith large individuals in males than in females. In "normal"species, male preference for large (i.e. more fecund) femalesis advantageous, but in this system such a choice can resultin mating with the larger LR females. With respect to the structureand dynamics of mixed populations, we discuss that the observed female preference is consistent with the higher mating successof LL males found in nature. Hence, mate female choice is astrong candidate for a mechanism promoting coexistence of thesperm-dependent hybrid and its sexual host. This confirms predictionsfrom previous theoretical models.     

Expression of N-methyl-D-aspartate (R)(GluN2B) - subunits in the brain structures of rats selected for low and high anxiety

In this paper, we studied differences in the density of N-methyl-D-aspartate (NMDA) receptor GluN2B subunits in the brains of low (LR) and high (HR) anxiety rats subjected to extinction trials and re-learning of a conditioned fear response, modeling a natural course of anxiety disorders. Classifications of animals as LR or HR was determined by fear-induced freezing responses in the contextual fear test. Increased basal concentrations of GluN2B subunits were observed in the amygdala of HR rats as compared to the unconditioned control group by Western blot analysis. Re-exposure of HR animals to the fear-conditioned context resulted in elevated concentrations of GluN2B subunits in the amygdala, hippocampus and the prefrontal cortex compared to LR rats as well as in the hippocampus and prefrontal cortex vs. the control group. In addition, it was shown that re-test of a conditioned fear increased the number of cells expressing GluN2B subunits in the basolateral amygdala, dentate gyrus of the hippocampus and secondary motor cortex (M2) in the HR group relative to the LR group. Together, these data suggest that animals that are more anxious have altered patterns of GluN2B subunit expression in the frontal cortex and limbic structures, which control emotional behaviour.     

Gene identification and expression analysis of 86,136 Expressed Sequence Tags (EST) from the rice genome

Expressed Sequence Tag (EST) analysis has pioneered genome-wide gene discovery and expression profiling. In order to establish a gene expression index in the rice cultivar indica, we sequenced and analyzed 86,136 ESTs from nine rice cDNA libraries from the super hybrid cultivar LYP9 and its parental cultivars. We assembled these ESTs into 13,232 contigs and leave 8,976 singletons. Overall, 7,497 sequences were found similar to the existing sequences in GenBank and 14,711 are novel. These sequences are classified by molecular function, biological process and pathways according to the Gene Ontology. We compared our sequenced ESTs with the publicly available 95,000 ESTs from japonica, and found little sequence variation, despite the large difference between genome sequences. We then assembled the combined 173,000 rice ESTs for further analysis. Using the pooled ESTs, we compared gene expression in metabolism pathway between rice and Arabidopsis according to KEGG. We further profiled gene expression pattern     

Defensive behaviour and its inheritance in the anabantoid fish, Macropodus opercularis and Macropodus opercularis concolor

In this preliminary study defense behaviour patterns (fear responses) are described in two closely related, behaviourally different inbred labyrinth fish subspecies and in their F₁ generation. The subspecies M. opercularis (characterized briefly by “active escape”) and M. opercularis concolor (characterized by “passive escape”) showed specific differences in the manifestation of certain defense behaviour patterns. In the F₁ hybrid generation dominance and overdominance of M. opercularis was found in most defense behaviour patterns. Analysing the frequencies and sequences of movement patterns it could be shown that defensive behaviour is not a random or entirely “plastic” process but that there is sequential linkage between the patterns and they form characteristic clusters. Our results suggest that manifestations of different patterns are under genetic control and presumably, genetic determination of certain patterns is not very complex. Attempts were made to determine whole brain noradrenaline, serotonine and dopamine levels of the two subspecies and a significant difference was found in the noradrenaline content.     

一株抗蓝舌病病毒8型VP2蛋白单克隆抗体识别的线性抗原表位的鉴定

为研究本实验室制备的一株抗蓝舌病病毒8型(BTV-8)VP2蛋白的单克隆抗体(MAb)3G11识别的B细胞抗原表位,利用噬菌体肽库展示技术对3G11识别的抗原表位进行筛选并鉴定。经过4轮淘选后挑取蓝斑测序,测序结果经分析后获得KLLAT序列,与BTV-8 VP2蛋白氨基酸序列比对后获得共同的短肽序列为283LL284;合成4种短肽序列:KLLAA、KALAT、KLAAT和KLLAT,与3G11细胞上清和腹水分别进行间接ELISA鉴定,结果表明,短肽KLLAA和KLLAT与3G11细胞上清及腹水具有较强的结合能力;与24种BTV标准阳性血清反应结果表明,这两种短肽都可与BTV-8阳性血清发生特异性反应;序列分析结果可见,该表位的氨基酸序列283LL284在不同来源的BTV-8毒株间保守,确定283LL284为MAb3G11识别抗原表位的关键氨基酸。本研究为建立8型BTV特异性的免疫学检测方法和相关病毒蛋白的功能研究奠定了基础。     

Sequence learning recodes cortical representations instead of strengthening initial ones

We contrast two computational models of sequence learning. The associative learner posits that learning proceeds by strengthening existing association weights. Alternatively, recoding posits that learning creates new and more efficient representations of the learned sequences. Importantly, both models propose that humans act as optimal learners but capture different statistics of the stimuli in their internal model. Furthermore, these models make dissociable predictions as to how learning changes the neural representation of sequences. We tested these predictions by using fMRI to extract neural activity patterns from the dorsal visual processing stream during a sequence recall task. We observed that only the recoding account can explain the similarity of neural activity patterns, suggesting that participants recode the learned sequences using chunks. We show that associative learning can theoretically store only very limited number of overlapping sequences, such as common in ecological working memory tasks, and hence an efficient learner should recode initial sequence representations.     

Unpredictability of vigilance in two sympatric Tibetan ungulates

Vigilance is important for anti-predation, and different animals adopt different vigilance strategies. Instantaneous and sequential randomness in vigilance behavior are two main principles for the classic Pulliam model (1973). Given this context, we studied the vigilance behaviors in two wild cloven-hoofed animals, the Tibetan antelope (Pantholops hodgsonii) and the Tibetan gazelle (Procapra picticaudata) on Qinghai–Tibet Plateau, to explore if the two randomness principles work across species. The results showed that the distribution of inter-scan intervals of both Tibetan antelope and Tibetan gazelle followed the negative exponential distribution; inter-scans of both Tibetan antelope and Tibetan gazelle were unrelated with their previous scan, and most sequences of inter-scan intervals could be considered as random organized or unpredictable. In conclusion, the vigilance patterns of Tibetan antelope and Tibetan gazelle followed instantaneous randomness and sequential randomness of Pulliam model. A random vigilance strategy might be the best choice for Tibetan ungulates, and how to distinguish the social vigilance from anti-predator vigilance is an important issue for future research.     

Protein loops on structurally similar scaffolds: database and conformational analysis

A general problem in comparative modeling and protein design is the conformational evaluation of loops with a certain sequence in specific environmental protein frameworks. Loops of different sequences and structures on similar scaffolds are common in the Protein Data Bank (PDB). In order to explore both structural and sequential diversity of them, a data base of loops connecting similar secondary structure fragments is constructed by searching the data base of families of structurally similar proteins and PDB. A total of 84 loop families having 2-13 residues are found among the well-determined structures of resolution better than 2.5 A. Eight alpha-alpha, 20 alpha-beta, 19 beta-alpha, and 37 beta-beta families are identified. Every family contains more than 5 loop motifs. In each family, no loops share same sequence and all the frameworks are well superimposed. Forty-three new loop classes are distinguished in the data base. The structural variability of loops in homologous proteins are examined and shown in 44 families. Motif families are characterized with geometric parameters and sequence patterns. The conformations of loops in each family are clustered into subfamilies using average linkage cluster analysis method. Information such as geometric properties, sequence profile, sequential and structural variability in loop, structural alignment parameters, sequence similarities, and clustering results are provided. Correlations between the conformation of loops and loop sequence, motif sequence, and global sequence of PDB chain are examined in order to find how loop structures depend on their sequences and how they are affected by the local and global environment. Strong correlations (R > 0.75) are only found in 24 families. The best R value is 0.98. The data base is available through the Internet.     

Analysis of oviposition behaviour in the parasitoidEpidinocarsis lopezi (Hym.: Encyrtidae): Comparison of flow charts on factorial maps

Females ofEpidinocarsis lopezi (De Santis) are presented with groups of unparasitized hosts or groups containing different ratios of parasitized hosts (Phenacoccus manihoti). Oviposition behaviour sequences obtained in various situations are filmed and split into units of behaviour or patterns. The succession of patterns is analyzed and translated into flow charts on factorial maps characteristic of each type of sequence. Comparison of flow charts reveals host discrimination by female parasitoids since the relative importance of behaviour patterns is modified according to the level of parasitized hosts encountered; it also gives clues to the strategy adopted by the female parasitoid during the search of a patch. In addition, the analysis divides the oviposition sequence into three separate patterns, specific to host search, oviposition act and post-oviposition behaviour. This series of patterns is closely related to factorial axes which indicates the fundamental trends of oviposition behaviour.     

Evolution of Courtship Behaviour Patterns and Reproductive Isolation in the Desmognathus ochrophaeus Complex

The extent to which differences in courtship behaviour patterns act as mechanisms of reproductive isolation is critical to understanding both speciation and the evolution of these behaviour patterns. While numerous studies have investigated intraspecific and interspecific differences in courtship, fewer interpret results in a phylogenetic framework. We describe and analyse geographic variation in the courtship behaviour patterns of the Allegheny Dusky salamander ( Desmognathus ochrophaeus ). We then examine courtship among closely related species in the D. ochrophaeus complex in a phylogenetic context. We found that populations of D. ochrophaeus separated by extensive geographic distances show little variation in courtship behaviour patterns and are sexually compatible. This contrasts with significant levels of sexual isolation between D. ochrophaeus and other species in the complex. Mapping behaviour patterns onto a phylogeny that we generated from cytochrome b sequences indicates that two behaviour patterns present in the courtship sequence of other members in the complex have either been lost in D. ochrophaeus or gained independently in other species in the complex. Loss of these behaviour patterns may result in reproductive isolation between D. ochrophaeus and its sister taxon, D. orestes .