From genomes to morphology: a view from amphioxus

Holland, P.W.H. 2010. From genomes to morphology: a view from amphioxus. —Acta Zoologica (Stockholm) 91 : 81–86 As complete genome sequences are determined from an ever‐increasing number of animal species, new opportunities are arising for comparative biology. For zoologists interested in the evolution of shape and form, however, there is a problem. The link between genome sequence and morphology is not direct and is obfuscated by complex and evolving genetic pathways, even when conserved regulatory genes are considered. Nonetheless, a large‐scale comparison of genome sequences between extant chordates reveals an intriguing parallel between genotypic and phenotypic evolution. Tunicates have highly altered genomes, with loss of ancestral genes and shuffled genetic arrangements, while vertebrate genomes are also derived through gene loss and genome duplication. The recently sequenced amphioxus genome, in contrast, reveals much greater stasis on the cephalochordate lineage, in parallel to a less derived body plan. The opportunities and challenges for relating genome evolution to morphological evolution are discussed.     

From sensory evidence to a motor command

New insight into how the brain makes a decision has come from a study of the effects of the decision-making process on an eye movement evoked by electrical stimulation of the frontal cortex. The accumulation of sensory evidence was found to cause a gradual commitment toward a choice.     

CD1 antigen presentation: how it works

The classic concept of self-non-self discrimination by the immune system focused on the recognition of fragments from proteins presented by classical MHC molecules. However, the discovery of MHC-class-I-like CD1 antigen-presentation molecules now explains how the immune system also recognizes the abundant and diverse universe of lipid-containing antigens. The CD1 molecules bind and present amphipathic lipid antigens for recognition by T-cell receptors. Here, we outline the recent advances in our understanding of how the processes of CD1 assembly, trafficking, lipid-antigen binding and T-cell activation are achieved and the new insights into how lipid antigens differentially elicit CD1-restricted innate and adaptive T-cell responses.     

From genomes to societies: a holistic view of determinants of human health

1. Download : Download high-res image (187KB)
2. Download : Download full-size image

     

From hierarchy to network: a richer view of evidence for evidence-based medicine

Evidence-based medicine (EBM) advocates the improvement of patient care through the use of current best research evidence in medical decision making. In practice, "best evidence" generally refers to where a study fits on a hierarchy of evidence, which places randomized controlled trials (RCTs) and other population-level research above laboratory research. Because population research is concerned primarily with average results obtained from large groups of people, ranking evidence on the basis of its place in the hierarchy is shortsighted and ultimately limits the ability of research results to inform the care of individual patients. The history and methodology of epidemiology reveals a close relationship between population-level and laboratory research; both types of research are necessary if we are to understand the causes of a disease. What EBM does not take into account in its hierarchy of evidence is that the same thing is true for research on the safety and efficacy of medical interventions. To maximize the information that clinical research can provide for clinical care, RCTs should be designed to elucidate within-group variability. This can only be done if the hierarchy of evidence is replaced by a network that takes into account the relationship between epidemiological and laboratory research.     

From genes to networks: in systematic points of view

We present a report of the BIOCOMP'10 - The 2010 International Conference on Bioinformatics & Computational Biology and other related work in the area of systems biology.     

From response to stimulus: adaptive sampling in sensory physiology

Sensory systems extract behaviorally relevant information from a continuous stream of complex high-dimensional input signals. Understanding the detailed dynamics and precise neural code, even of a single neuron, is therefore a non-trivial task. Automated closed-loop approaches that integrate data analysis in the experimental design ease the investigation of sensory systems in three directions: First, adaptive sampling speeds up the data acquisition and thus increases the yield of an experiment. Second, model-driven stimulus exploration improves the quality of experimental data needed to discriminate between alternative hypotheses. Third, information-theoretic data analyses open up novel ways to search for those stimuli that are most efficient in driving a given neuron in terms of its firing rate or coding quality. Examples from different sensory systems show that, in all three directions, substantial progress can be achieved once rapid online data analysis, adaptive sampling, and computational modeling are tightly integrated into experiments.     

From signaling to function: how strigolactones regulate plant development

Science China Life Sciences -     

From hominins to humans: how sapiens became behaviourally modern

This paper contributes to a debate in the palaeoarchaeological community about the major time-lag between the origin of anatomically modern humans and the appearance of typically human cultural behaviour. Why did humans take so long—at least 100 000 years—to become ‘behaviourally modern’? The transition is often explained as a change in the intrinsic cognitive competence of modern humans: often in terms of a new capacity for symbolic thought, or the final perfection of language. These cognitive breakthrough models are not satisfactory, for they fail to explain the uneven palaeoanthropological record of human competence. Many supposed signature capacities appear (and then disappear) before the supposed cognitive breakthrough; many of the signature capacities disappear again after the breakthrough. So, instead of seeing behavioural modernity as a simple reflection of a new kind of mind, this paper presents a niche construction conceptual model of behavioural modernity. Humans became behaviourally modern when they could reliably transmit accumulated informational capital to the next generation, and transmit it with sufficient precision for innovations to be preserved and accumulated. In turn, the reliable accumulation of culture depends on the construction of learning environments, not just intrinsic cognitive machinery. I argue that the model is (i) evolutionarily plausible: the elements of the model can be assembled incrementally, without implausible selective scenarios; (ii) the model coheres with the broad palaeoarchaeological record; (iii) the model is anthropologically and ethnographically plausible; and (iv) the model is testable, though only in coarse, preliminary ways.     

From competition to facilitation: how tree species respond to neighbourhood diversity

Studies on tree communities have demonstrated that species diversity can enhance forest productivity, but the driving mechanisms at the local neighbourhood level remain poorly understood. Here, we use data from a large‐scale biodiversity experiment with 24 subtropical tree species to show that neighbourhood tree species richness generally promotes individual tree productivity. We found that the underlying mechanisms depend on a focal tree's functional traits: For species with a conservative resource‐use strategy diversity effects were brought about by facilitation, and for species with acquisitive traits by competitive reduction. Moreover, positive diversity effects were strongest under low competition intensity (quantified as the total basal area of neighbours) for acquisitive species, and under high competition intensity for conservative species. Our findings demonstrate that net biodiversity effects in tree communities can vary over small spatial scales, emphasising the need to consider variation in local neighbourhood interactions to better understand effects at the community level.     

From sensing cellular sterols to assembling sensory structures

The genome of the nematode C. elegans is peppered with novel genes belonging to a superfamily whose members function in cellular cholesterol homeostasis (Niemann-Pick C1) and Hedgehog signal transduction (Patched) and biogenesis (Dispatched). In this issue of Developmental Cell and an analysis of a pair of Patched- and Dispatched-related proteins in C. elegans extends the superfamily's repertoire to include the formation of tubular organs.