Action understanding: how, what and why

The mirror neuron system may help us understand how others act and what they do. A recent study has shown that consciously reflecting on their intentions additionally recruits mentalizing areas.     

Visual attention: the where,what, how and why of saliency

Attention influences the processing of visual information even in the earliest areas of primate visual cortex. There is converging evidence that the interaction of bottom-up sensory information and top-down attentional influences creates an integrated saliency map, that is, a topographic representation of relative stimulus strength and behavioral relevance across visual space. This map appears to be distributed across areas of the visual cortex, and is closely linked to the oculomotor system that controls eye movements and orients the gaze to locations in the visual scene characterized by a high salience.     

Neurohormonal-cytokine interactions: implications for inflammation, common human diseases and well-being

The neuroendocrine system affects the immune system through the neuroendocrine humoral outflow via the pituitary, and through direct neuronal influences via the sympathetic, parasympathetic (cholinergic) and peptidergic/sensory innervation of peripheral tissues. Circulating hormones or locally released neurotransmitters and neuropeptides regulate major immune functions, such as antigen presentation, antibody production, lymphocyte activity, proliferation and traffic, and the secretion of cytokines including the selection of T helper (Th)1 or Th2 cytokine responses. During inflammation, the activation of the stress system, through induction of a Th2 shift protects the organism from systemic "overshooting" with Th1/pro-inflammatory cytokines. Under certain conditions, however, stress hormones, substance P, ATP and the activation of the corticotropin-releasing hormone/substance P-histamine axis may actually facilitate inflammation, through induction of interleukin (IL)-1, IL-6, IL-8, IL-18, tumor necrosis factor (TNF)-alpha and CRP production. Thus, a dysfunctional neuroendocrine-immune interface associated with abnormalities of the 'systemic anti-inflammatory feedback' and/or 'hyperactivity' of the local pro-inflammatory factors may play a role in the pathogenesis of atopic/allergic and autoimmune diseases, obesity, depression and atherosclerosis. Better understanding of the neuroendocrine control of inflammation may provide critical insights into mechanisms underlying a variety of common human immune-related diseases.     

Pseudouridine in RNA: what, where, how, and why

Pseudouridine (5-ribosyluracil) is a ubiquitous yet enigmatic constituent of structural RNAs (transfer, ribosomal, small nuclear, and small nucleolar). Although pseudouridine (psi) was the first modified nucleoside to be discovered in RNA, and is the most abundant, its biosynthesis and biological roles have remained poorly understood since its identification as a fifth nucleoside in RNA. Recently, a combination of biochemical, biophysical, and genetic approaches has helped to illuminate the structural consequences of psi in polyribonucleotides, the biochemical mechanism of U-->psi isomerization in RNA, and the role of modification enzymes (psi synthases) and box H/ACA snoRNAs, a class of eukaryotic small nucleolar RNAs, in the site-specific biosynthesis of psi. Through its unique ability to coordinate a structural water molecule via its free N1-H, psi exerts a subtle but significant rigidifying influence on the nearby sugar-phosphate backbone and also enhances base stacking. These effects may underlie the biological role of most (but perhaps not all) of the psi residues in RNA. Certain genetic mutants lacking specific psi residues in tRNA or rRNA exhibit difficulties in translation, display slow growth rates, and fail to compete effectively with wild-type strains in mixed culture. In particular, normal growth is severely compromised in an Escherichia coli mutant deficient in a pseudouridine synthase responsible for the formation of three closely spaced psi residues in the mRNA decoding region of the 23S rRNA. Such studies demonstrate that pseudouridylation of RNA confers an important selective advantage in a natural biological context.     

Plant MAP kinase pathways: how many and what for?

Mitogen activated protein kinases (MAPK) are important mediators in signal transmission, connecting the perception of external stimuli to cellular responses. MAPK cascades are involved in signalling various biotic and abiotic stresses, like wounding and pathogen infection, temperature stress or drought, but also some plant hormones, such as ethylene and auxin. Moreover, MAPKs have been implicated in cell cycle and developmental processes. In Arabidopsis mutant screens and in vivo assays several components of plant MAPK cascades have been identified. This review compares results obtained from functional analyses of MAPK cascades in plants with recent data obtained from searching the complete Arabidopsis genome. This analysis reveals that plants have an overall of 24 MAPK pathways of which only a small subset has been studied so far.     

The what, where, how and why of gene ontology--a primer for bioinformaticians

With high-throughput technologies providing vast amounts of data, it has become more important to provide systematic, quality annotations. The Gene Ontology (GO) project is the largest resource for cataloguing gene function. Nonetheless, its use is not yet ubiquitous and is still fraught with pitfalls. In this review, we provide a short primer to the GO for bioinformaticians. We summarize important aspects of the structure of the ontology, describe sources and types of functional annotations, survey measures of GO annotation similarity, review typical uses of GO and discuss other important considerations pertaining to the use of GO in bioinformatics applications.     

Smart phone, smart science: how the use of smartphones can revolutionize research in cognitive science

Investigating human cognitive faculties such as language, attention, and memory most often relies on testing small and homogeneous groups of volunteers coming to research facilities where they are asked to participate in behavioral experiments. We show that this limitation and sampling bias can be overcome by using smartphone technology to collect data in cognitive science experiments from thousands of subjects from all over the world. This mass coordinated use of smartphones creates a novel and powerful scientific "instrument" that yields the data necessary to test universal theories of cognition. This increase in power represents a potential revolution in cognitive science.     

The why,what, where,when and how of goal-directed choice: neuronal and computational principles

The central problems that goal-directed animals must solve are: ‘What do I need and Why, Where and When can this be obtained, and How do I get it?'' or the H4W problem. Here, we elucidate the principles underlying the neuronal solutions to H4W using a combination of neurobiological and neurorobotic approaches. First, we analyse H4W from a system-level perspective by mapping its objectives onto the Distributed Adaptive Control embodied cognitive architecture which sees the generation of adaptive action in the real world as the primary task of the brain rather than optimally solving abstract problems. We next map this functional decomposition to the architecture of the rodent brain to test its consistency. Following this approach, we propose that the mammalian brain solves the H4W problem on the basis of multiple kinds of outcome predictions, integrating central representations of needs and drives (e.g. hypothalamus), valence (e.g. amygdala), world, self and task state spaces (e.g. neocortex, hippocampus and prefrontal cortex, respectively) combined with multi-modal selection (e.g. basal ganglia). In our analysis, goal-directed behaviour results from a well-structured architecture in which goals are bootstrapped on the basis of predefined needs, valence and multiple learning, memory and planning mechanisms rather than being generated by a singular computation.     

Embodied economics: how bodily information shapes the social coordination dynamics of decision-making

To date, experiments in economics are restricted to situations in which individuals are not influenced by the physical presence of other people. In such contexts, interactions remain at an abstract level, agents guessing what another person is thinking or is about to decide based on money exchange. Physical presence and bodily signals are therefore left out of the picture. However, in real life, social interactions (involving economic decisions or not) are not solely determined by a person''s inference about someone else''s state-of-mind. In this essay, we argue for embodied economics: an approach to neuroeconomics that takes into account how information provided by the entire body and its coordination dynamics influences the way we make economic decisions. Considering the role of embodiment in economics—movements, posture, sensitivity to mimicry and every kind of information the body conveys—makes sense. This is what we claim in this essay which, to some extent, constitutes a plea to consider bodily interactions between agents in social (neuro)economics.     

Plant genotype shapes ant-aphid interactions: implications for community structure and indirect plant defense

Little is known about the mechanisms by which plant genotype shapes arthropod community structure. In a field experiment, we measured the effects of milkweed (Asclepias syriaca) genotype and ants on milkweed arthropods. Populations of the ant-tended aphid Aphis asclepiadis and the untended aphid Myzocallis asclepiadis varied eight- to 18-fold among milkweed genotypes, depending on aphid species and whether ants were present. There was no milkweed effect on predatory arthropods. Ants increased Aphis abundance 59%, decreased Myzocallis abundance 52%, and decreased predator abundance 56%. Milkweed genotype indirectly influenced ants via direct effects on Aphis and Myzocallis abundance. Milkweed genotype also modified ant-aphid interactions, influencing the number of ants attracted per Aphis and Myzocallis. While ant effects on Myzocallis were consistently negative, effects on Aphis ranged from antagonistic to mutualistic among milkweed genotypes. As a consequence of milkweed effects on ant-aphid interactions, ant abundance varied 13-fold among milkweed genotypes, and monarch caterpillar survival was negatively correlated with genetic variation in ant abundance. We speculate that heritable variation in milkweed phloem sap drives these effects on aphids, ants, and caterpillars. In summary, milkweed exerts genetic control over the interactions between aphids and an ant that provides defense against foliage-feeding caterpillars.     

Private heat for public warmth: how huddling shapes individual thermogenic responses of rabbit pups

Background

Within their litter, young altricial mammals compete for energy (constraining growth and survival) but cooperate for warmth. The aim of this study was to examine the mechanisms by which huddling in altricial infants influences individual heat production and loss, while providing public warmth. Although considered as a textbook example, it is surprising to note that physiological mechanisms underlying huddling are still not fully characterised.

Methodology/Principal Findings

The brown adipose tissue (BAT) contribution to energy output was assessed as a function of the ability of rabbit (Oryctolagus cuniculus) pups to huddle (placed in groups of 6 and 2, or isolated) and of their thermoregulatory capacities (non-insulated before 5 days old and insulated at ca. 10 days old). BAT contribution of pups exposed to cold was examined by combining techniques of infrared thermography (surface temperature), indirect calorimetry (total energy expenditure, TEE) and telemetry (body temperature). Through local heating, the huddle provided each pup whatever their age with an ambient “public warmth” in the cold, which particularly benefited non-insulated pups. Huddling allowed pups facing a progressive cold challenge to buffer the decreasing ambient temperature by delaying the activation of their thermogenic response, especially when fur-insulated. In this way, huddling permitted pups to effectively shift from a non-insulated to a pseudo-insulated thermal state while continuously allocating energy to growth. The high correlation between TEE and the difference in surface temperatures between BAT and back areas of the body reveals that energy loss for non-shivering thermogenesis is the major factor constraining the amount of energy allocated to growth in non-insulated altricial pups.

Conclusions/Significance

By providing public warmth with minimal individual costs at a stage of life when pups are the most vulnerable, huddling buffers cold challenges and ensures a constant allocation of energy to growth by reducing BAT activation.     

Underlying regularity in the shapes of nucleoids of Escherichia coli: implications for nucleoid organization and partition

The genomic DNA of Escherichia coli is localized in one or a few compact nucleoids. Nucleoids in rapidly grown cells appear in complex shapes; the relationship of these shapes to underlying arrangements of the DNA is of structural interest and of potential importance in gene localization and nucleoid partition studies. To help assess this variation in shape, limited three-dimensional information on individual nucleoids was obtained by DNA fluorescence microscopy of cells as they reoriented in solution or by optical sectioning. These techniques were also applied to enlarged nucleoids within swollen cells or spheroplasts. The resulting images indicated that much of the apparent variation was due to imaging from different directions and at different focal planes of more regular underlying nucleoid shapes. Nucleoid images could be transformed into compact doublet shapes by exposure of cells to chloramphenicol or puromycin, consistent with a preexisting bipartite nucleoid structure. Isolated nucleoids and nucleoids in stationary-phase cells also assumed a doublet shape, supporting such a structure. The underlying structure is suggested to be two subunits joined by a linker. Both the subunits and the linker appear to deform to accommodate the space available within cells or spheroplasts ("flexible doublet" model).