Localized brain activation related to the strength of auditory learning in a parrot

Parrots and songbirds learn their vocalizations from a conspecific tutor, much like human infants acquire spoken language. Parrots can learn human words and it has been suggested that they can use them to communicate with humans. The caudomedial pallium in the parrot brain is homologous with that of songbirds, and analogous to the human auditory association cortex, involved in speech processing. Here we investigated neuronal activation, measured as expression of the protein product of the immediate early gene ZENK, in relation to auditory learning in the budgerigar (Melopsittacus undulatus), a parrot. Budgerigar males successfully learned to discriminate two Japanese words spoken by another male conspecific. Re-exposure to the two discriminanda led to increased neuronal activation in the caudomedial pallium, but not in the hippocampus, compared to untrained birds that were exposed to the same words, or were not exposed to words. Neuronal activation in the caudomedial pallium of the experimental birds was correlated significantly and positively with the percentage of correct responses in the discrimination task. These results suggest that in a parrot, the caudomedial pallium is involved in auditory learning. Thus, in parrots, songbirds and humans, analogous brain regions may contain the neural substrate for auditory learning and memory.     

Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation

MOTIVATION: The whole genomes submitted to GenBank contain valuable information about the function of genes as well as the upstream sequences and whole cell expression provides valuable information on gene regulation. To utilize these large amounts of data for a biological understanding of the regulation of gene expression, new automatic methods for pattern finding are needed. RESULTS: Two word-analysis algorithms for automatic discovery of regulatory sequence elements have been developed. We show that sequence patterns correlated to whole cell expression data can be found using Kolmogorov-Smirnov tests on the raw data, thereby eliminating the need for clustering co-regulated genes. Regulatory elements have also been identified by systematic calculations of the significance of correlations between words found in the functional annotation of genes and DNA words occurring in their promoter regions. Application of these algorithms to the Saccharomyces cerevisiae genome and publicly available DNA array data sets revealed a highly conserved 9-mer occurring in the upstream regions of genes coding for proteasomal subunits. Several other putative and known regulatory elements were also found. AVAILABILITY: Upon request.     

Evolution of nucleosome occupancy: conservation of global properties and divergence of gene-specific patterns

To examine the role of nucleosome occupancy in the evolution of gene expression, we measured the genome-wide nucleosome profiles of four yeast species, three belonging to the Saccharomyces sensu stricto lineage and the more distantly related Candida glabrata. Nucleosomes and associated promoter elements at C. glabrata genes are typically shifted upstream by ～20 bp, compared to their orthologs from sensu stricto species. Nonetheless, all species display the same global organization features first described for Saccharomyces cerevisiae: a stereotypical nucleosome organization along genes and a division of promoters into those that contain or lack a pronounced nucleosome-depleted region (NDR), with the latter displaying a more dynamic pattern of gene expression. Despite this global similarity, however, nucleosome occupancy at specific genes diverged extensively between sensu stricto and C. glabrata orthologs (～50 million years). Orthologs with dynamic expression patterns tend to maintain their lack of NDR, but apart from that, sensu stricto and C. glabrata orthologs are nearly as similar in nucleosome occupancy patterns as nonorthologous genes. This extensive divergence in nucleosome occupancy contrasts with a conserved pattern of gene expression. Thus, while some evolutionary changes in nucleosome occupancy contribute to gene expression divergence, nucleosome occupancy often diverges extensively with apparently little impact on gene expression.     

Incidence of and risk factors for nodding off at scientific sessions

We conducted a surreptitious, prospective, cohort study to explore how often physicians nod off during scientific meetings and to examine risk factors for nodding off. After counting the number of heads falling forward during 2 days of lectures, we calculated the incidence density curves for nodding-off episodes per lecture (NOELs) and assessed risk factors using logistic regression analysis. In this article we report our eye-opening results and suggest ways speakers can try to avoid losing their audience.Despite their known inefficiency, lectures (“a means of transferring notes from the pages of the speaker to the pages of the audience, without going through the mind of either”) continue to predominate as a means of helping physicians learn their trade. At a recent 2-day lecture series, we noticed that many of the attendees around us were nodding off, including one of our coauthors (C.J.P.). After awakening him, we decided to study the boredom itself by measuring how often physicians nodded off during the lectures and assessing risk factors for this behaviour.     

Pattern learning by honeybees: conditioning procedure and recognition strategy

In recognizing a pattern, honeybees Apis mellifera, may focus either on its ventral frontal part, or on the whole frontal image. We asked whether the conditioning procedure used to train the bees to a pattern determines the recognition strategy employed. Bees were trained with the same patterns presented vertically on the back walls of a Y maze. Conditioning was either absolute, that is, bees should learn to choose a rewarded pattern when there is no alternative, or differential, that is, bees should learn to choose a rewarded pattern that is paired with a different, nonrewarded one. Bees used different pattern recognition strategies depending on the conditioning procedure: absolute conditioning restricted recognition to the lower half whilst differential conditioning extended it to the whole pattern. Bees trained with absolute conditioning saw and learned the features of the upper part of the trained patterns, but assigned more weight to the lower part. Bees trained with differential conditioning learned not only the features of the reinforced stimulus in an excitatory way, but also those of the nonreinforced one in an inhibitory way. Thus, conditioning tasks that involve not only excitatory acquisition of the conditioned stimulus per se, but also discrimination of nonreinforced stimuli, result in an increase in the visual field assigned to the recognition task. Conditioning tasks that involve only excitatory acquisition of the rewarded stimulus result in a higher weighting of the lower pattern half and thus in a more reduced field assigned to the recognition task. This difference may reflect that existing between a conditioned and an incidental behavioural modification. Copyright 1999 The Association for the Study of Animal Behaviour.     

Are Individual Differences in Reading Speed Related to Extrafoveal Visual Acuity and Crowding?

Readers differ considerably in their speed of self-paced reading. One factor known to influence fixation durations in reading is the preprocessing of words in parafoveal vision. Here we investigated whether individual differences in reading speed or the amount of information extracted from upcoming words (the preview benefit) can be explained by basic differences in extrafoveal vision—i.e., the ability to recognize peripheral letters with or without the presence of flanking letters. Forty participants were given an adaptive test to determine their eccentricity thresholds for the identification of letters presented either in isolation (extrafoveal acuity) or flanked by other letters (crowded letter recognition). In a separate eye-tracking experiment, the same participants read lists of words from left to right, while the preview of the upcoming words was manipulated with the gaze-contingent moving window technique. Relationships between dependent measures were analyzed on the observational level and with linear mixed models. We obtained highly reliable estimates both for extrafoveal letter identification (acuity and crowding) and measures of reading speed (overall reading speed, size of preview benefit). Reading speed was higher in participants with larger uncrowded windows. However, the strength of this relationship was moderate and it was only observed if other sources of variance in reading speed (e.g., the occurrence of regressive saccades) were eliminated. Moreover, the size of the preview benefit—an important factor in normal reading—was larger in participants with better extrafoveal acuity. Together, these results indicate a significant albeit moderate contribution of extrafoveal vision to individual differences in reading speed.     

Als ‘A’ niet meer als ‘a’ wordt herkend. Een analyse van verworven woordblindheid

A right-handed patient, aged 72, manifested alexia without agraphia, a right homonymous hemianopia and an impaired ability to identify visually presented objects. He was completely unable to read words aloud and severely deficient in naming visually presented letters. He responded to orthographic familiarity in the lexical decision tasks of the Psycholinguistic Assessments of Language Processing in Aphasia (PALPA) rather than to the lexicality of the letter strings. He was impaired at deciding whether two letters of different case (e.g., A, a) are the same, though he could detect real letters from made-up ones or from their mirror image. Consequently, his core deficit in reading was posited at the level of the abstract letter identifiers. When asked to trace a letter with his right index finger, kinesthetic facilitation enabled him to read letters and words aloud. Though he could use intact motor representations of letters in order to facilitate recognition and reading, the slow, sequential and error-prone process of reading letter by letter made him abandon further training.     

Negative selection and computer models of the joint evolution of the patterns of polygenes,transposable elements,and origin identity labels

Computer simulation of the population dynamics of the genomic patterns of polygenes, transposable elements (TEs), and origin identity labels (OILs) in the course of negative selection for an additive quantitative trait has been performed. It was demonstrated that active polygene alleles disappear very rapidly, whereas the patterns of TEs and OILs continue their evolution determined by strict selective inbreeding and gene drift. Dendrograms of the patterns of polygenes, TEs, and OILs were constructed for all generations. It was demonstrated that the final consensus pattern of OILs consists of the fragments of the original patterns, which contain neither active polygene alleles nor modifier or marker TEs. Neutral TE copies were present in the final pattern, as should be expected in the case of gene drift. Inbreeding coefficient increased steadily but by generation 100 reached values higher than 0.9. All other parameters and initial conditions being the same, the responses to negative and positive selections were asymmetric.     

Computer Simulation of Concerted Evolution of Patterns of Polygenes, Transposable Elements, and Origin Identity Labels: Negative Selection

Computer simulation of the population dynamics of the genomic patterns of polygenes, transposable elements (TEs), and origin identity labels (OILs) in the course of negative selection for an additive quantitative trait has been performed. It was demonstrated that active polygene alleles disappear very rapidly, whereas the patterns of TEs and OILs continue their evolution determined by strict selective inbreeding and gene drift. Dendrograms of the patterns of polygenes, TEs, and OILs were constructed for all generations. It was demonstrated that the final consensus pattern of OILs consists of the fragments of the original patterns, which contain neither active polygene alleles nor modifier or marker TEs. Neutral TE copies were present in the final pattern, as should be expected in the case of gene drift. Inbreeding coefficient increased steadily but by generation 100 reached values higher than 0.9. All other parameters and initial conditions being the same, the responses to negative and positive selections were asymmetric.     

Discrimination of coloured patterns by honeybees through chromatic and achromatic cues

We investigated pattern discrimination by worker honeybees, Apis mellifera, focusing on the roles of spectral cues and the angular size of patterns. Free-flying bees were trained to discriminate concentric patterns in a Y-maze. The rewarded pattern could be composed of either a cyan and a yellow colour, which presented both different chromatic and achromatic L-receptor contrast, or an orange and a blue colour, which presented different chromatic cues, but the same L-receptor contrast. The non-rewarded alternative was either a single-coloured disc with the colour of the central disc or the surrounding ring of the pattern, a checkerboard pattern with non-resolvable squares, the reversed pattern, or the elements of the training pattern (disc or ring alone). Bees resolved and learned both colour elements in the rewarded patterns and their spatial properties. When the patterns subtended large visual angles, this discrimination used chromatic cues only. Patterns with yellow or orange central discs were generalised toward the yellow and orange colours, respectively. When the patterns subtended a visual angle close to the detection limit and L-receptor contrast was mediating discrimination, pattern perception was reduced: bees perceived only the pattern element with higher contrast.     

Application of serum protein fingerprint in diagnosis of papillary thyroid carcinoma

To find new biomarkers and establish serum protein fingerprint models for early diagnosis and preoperative staging of papillary thyroid carcinoma, we employed SELDI-TOF-MS and bioinformatics tools. A total of 116 samples were analyzed in this study. The first 80 samples were analyzed by SELDI-TOF-MS and two biomarker patterns were identified. Pattern 1 distinguishes patients with papillary thyroid carcinoma from healthy individuals. Pattern 2 distinguishes papillary thyroid carcinoma from benign thyroid nodes. The remaining 29 samples were analyzed on the second day and served as an independent test set. The analysis of this independent test set yielded a specificity of 80.0% and a sensitivity of 88.9% for pattern 1 and a specificity of 80.0% and a sensitivity of 80.0% for pattern 2. Two additional biomarker patterns were identified to distinguish different stages of the papillary thyroid carcinoma (pattern 3) with an accuracy of 77.1% and different pathological types of thyroid carcinoma (pattern 4) with an accuracy of 88.1%. Taken together, the SELDI-TOF-MS technique combined with bioinformatics approaches can not only facilitate the discovery of better biomarkers for papillary thyroid carcinoma but also provide a useful tool for molecular diagnosis in the future.     

Sequence organisation in nuclear DNA from Physarum polycephalum: Genomic organisation of DNA segments containing foldback sequences

DNA clones containing foldback sequences, derived from Physarum polycephalum nuclear DNA, can be classified according to their pattern of hydridisation to Southern blots of genomic DNA. One group of DNA clones map to unique DNA loci when used as a probe to restriction digests of Physarum nuclear DNA. These cloned segments appear to contain dispersed repetitive sequence elements located at many hundreds of sites in the genome. Similar patterns of hybridisation are generated when these cloned DNA probes are annealed to DNA restriction fragments of genomic DNA obtained from a number of different Physarum strains, indicating that no detectable alteration has occurred at these genomic loci subsequent to the divergence of the strains as a result of the introduction or deletion of mobile genetic elements. However, deletion of segments of some cloned DNA fragments occurs following their propagation in Escherichia coli. A second, distinct group of clones are shown to be derived from highly methylated segments of Physarum DNA which contain very abundant repetitive sequences with regular, though complex, arrangements of restriction sites at their various genomic locations. It is suggested that these DNA segments contain clustered repetitive sequence elements. The results lead to the conclusion that foldback elements in Physarum DNA are located in segments of the genome which display markedly different patterns of sequence organisation and degree of DNA methylation.     

Semantic integration by pattern priming: experiment and cortical network model

Neural network models describe semantic priming effects by way of mechanisms of activation of neurons coding for words that rely strongly on synaptic efficacies between pairs of neurons. Biologically inspired Hebbian learning defines efficacy values as a function of the activity of pre- and post-synaptic neurons only. It generates only pair associations between words in the semantic network. However, the statistical analysis of large text databases points to the frequent occurrence not only of pairs of words (e.g., “the way”) but also of patterns of more than two words (e.g., “by the way”). The learning of these frequent patterns of words is not reducible to associations between pairs of words but must take into account the higher level of coding of three-word patterns. The processing and learning of pattern of words challenges classical Hebbian learning algorithms used in biologically inspired models of priming. The aim of the present study was to test the effects of patterns on the semantic processing of words and to investigate how an inter-synaptic learning algorithm succeeds at reproducing the experimental data. The experiment manipulates the frequency of occurrence of patterns of three words in a multiple-paradigm protocol. Results show for the first time that target words benefit more priming when embedded in a pattern with the two primes than when only associated with each prime in pairs. A biologically inspired inter-synaptic learning algorithm is tested that potentiates synapses as a function of the activation of more than two pre- and post-synaptic neurons. Simulations show that the network can learn patterns of three words to reproduce the experimental results.     

Reversal Learning and Risk‐Averse Foraging Behavior in the Monarch Butterfly,Danaus plexippus (Lepidoptera: Nymphalidae)

Learning ability allows insects to respond to a variable environment, and to adjust their behaviors in response to positive or negative experiences. Pollinating insects readily learn to associate floral characteristics, such as color, shape, or pattern, with appetitive stimuli, such as the presence of a nectar reward. However, in nature pollinators may also encounter flowers that contain distasteful or toxic nectar, or offer highly variable nectar volumes, providing opportunities for aversive learning or risk‐averse foraging behavior. Whereas some bees learn to avoid flowers with unpalatable or unreliable nectar rewards, little is known about how Lepidoptera respond to such stimuli. We used a reversal learning paradigm to establish that monarch butterflies learn to discriminate against colored artificial flowers that contain salt solution, decreasing both number of probes and probing time on flowers of a preferred color and altogether avoiding artificial flowers of a non‐preferred color. In addition, when we offered butterflies artificial flowers of two different colors, both of which contained the same mean nectar volume but which differed in variance, the monarchs exhibited risk‐averse foraging: they probed the constant flowers significantly more than the variable ones, regardless of flower color or butterfly sex. Our results add to our understanding of butterfly foraging behavior, as they demonstrate that monarchs can respond to aversive as well as appetitive stimuli, and can also adjust their foraging behavior to avoid floral resources with high variance rewards.     

The effect of complexity on the discrimination of oriented bars by the honeybee (<Emphasis Type="Italic">Apis mellifera</Emphasis>)

Visual discrimination of black bars by honeybees was studied in a Y-choice apparatus with fixed vertical patterns at constant range. The problem is to discover how bees remember different degrees of complexity of the orientation cue. Previous conclusions with parallel gratings and single bars disagree. With broad bars versus orthogonal bars, the bees learn the orientation cue if the bars are centred at the same place, but they learn the position cue in the vertical direction when the bars are at different places on the two targets. With several bars on each target, the bees learn their orientation and positions. As fixed patterns increase in complexity, the bees follow a simple rule, to look only at the range of places where the cues were displayed. The frame of reference is disrupted when a black spot is added to the training pattern. There is abundant evidence that the bees do not re-assemble the pattern or learn shapes. The filters that detect the position and orientation cues are coarsely tuned, so that they respond in a graded way, but the memory of the range of directions of the cue, as seen from the point of choice, is more exact.     

斜茎黄芪根瘤菌结瘤基因nodA PCR扩增及PCR-RFLP分析

对采自我国北方地区的16株斜茎黄芪根瘤菌代表菌株的共同结瘤基因nodA进行了PCR扩增及PCR-RFLP分析研究。来自Mesorhizobium和Rhizobium系统发育分支的代表菌株都得到了nodA PCR扩增产物;而来自Agrobacterium系统发育分支的代表菌株都没有得到nodA PCR扩增产物。进一步的nodAPCR-RFLP分析结果表明斜茎黄芪根瘤菌具有很大的nodA基因遗传多样性,具有4种不同的16S rDNAPCR-RFLP遗传图谱类型的12株斜茎黄芪根瘤菌具有8种不同的nodA PCR-RFLP遗传图谱类型。但是斜茎黄芪根瘤菌nodA基因遗传多样性随种群而变化,来自M.septentrionale的具有相同的16S rDNA PCR-RFLP遗传图谱类型的4个代表菌株具有4种不同的nodA PCR-RFLP遗传图谱类型;而来自M.tempera-tum的具有相同的16S rDNA PCR-RFLP遗传图谱类型3个代表菌株则具有相同的nodA PCR-RFLP遗传图谱类型。此外,来自不同种的具有不同16S rDNA PCR-RFLP遗传图谱类型的菌株却具有相同的nodA PCR-RFLP遗传图谱类型,说明nodA基因可能在根瘤菌的不同种间发生了水平转移。     

Pattern Selection by Dynamical Biochemical Signals

The development of multicellular organisms involves cells to decide their fate upon the action of biochemical signals. This decision is often spatiotemporally coordinated such that a spatial pattern arises. The dynamics that drive pattern formation usually involve genetic nonlinear interactions and positive feedback loops. These complex dynamics may enable multiple stable patterns for the same conditions. Under these circumstances, pattern formation in a developing tissue involves a selection process: why is a certain pattern formed and not another stable one? Herein we computationally address this issue in the context of the Notch signaling pathway. We characterize a dynamical mechanism for developmental selection of a specific pattern through spatiotemporal changes of the control parameters of the dynamics, in contrast to commonly studied situations in which initial conditions and noise determine which pattern is selected among multiple stable ones. This mechanism can be understood as a path along the parameter space driven by a sequence of biochemical signals. We characterize the selection process for three different scenarios of this dynamical mechanism that can take place during development: the signal either 1) acts in all the cells at the same time, 2) acts only within a cluster of cells, or 3) propagates along the tissue. We found that key elements for pattern selection are the destabilization of the initial pattern, the subsequent exploration of other patterns determined by the spatiotemporal symmetry of the parameter changes, and the speeds of the path compared to the timescales of the pattern formation process itself. Each scenario enables the selection of different types of patterns and creates these elements in distinct ways, resulting in different features. Our approach extends the concept of selection involved in cellular decision-making, usually applied to cell-autonomous decisions, to systems that collectively make decisions through cell-to-cell interactions.