Human Complex Trait Genetics: Lifting the Lid of the Genomics Toolbox - from Pathways to Prediction

During the initial stages of the genome revolution human genetics was hugely successful in discovering the underlying genes for monogenic diseases. Over 3,000 monogenic diseases have been discovered with simple patterns of inheritance. The unravelling and identification of the genetic variants underlying complex or multifactorial traits, however, is proving much more elusive. There have been over 1,000 significant variants found for many quantitative and binary traits yet they explain very little of the estimated genetic variance or heritability evident from family analysis. There are many hypotheses as to why this might be the case. This apparent lack of information is holding back the clinical application of genetics and shedding doubt on whether more of the same will reveal where the remainder of the variation lies. Here we explore the current state of play, the types of variants we can detect and how they are currently exploited. Finally we look at the future challenges we must face to persuade the human genome to yield its secrets.     

Stand by me: Fibroblasts regulation of the intestinal epithelium during development and homeostasis

The epithelium of the small intestine is composed of a single layer of cells that line two functionally distinct compartments, the villi that project into the lumen of the gut and the crypts that descend into the underlying connective tissue. Stem cells are located in crypts, where they divide and give rise to transit-amplifying cells that differentiate into secretory and absorptive epithelial cells. Most differentiated cells travel upwards from the crypt towards the villus tip, where they shed into the lumen. While some of these cell behaviors are an intrinsic property of the epithelium, it is becoming evident that tight coordination between the epithelium and the underlying fibroblasts plays a critical role in tissue morphogenesis, stem-cell niche maintenance and regionalized gene expression along the crypt-villus axis. Here, we will review the current literature describing the interaction between epithelium and fibroblasts during crypt-villus axis development and intestinal epithelium renewal during homeostasis.     

The Distribution of Fitness Effects of Beneficial Mutations in Pseudomonas aeruginosa

Understanding how beneficial mutations affect fitness is crucial to our understanding of adaptation by natural selection. Here, using adaptation to the antibiotic rifampicin in the opportunistic pathogen Pseudomonas aeruginosa as a model system, we investigate the underlying distribution of fitness effects of beneficial mutations on which natural selection acts. Consistent with theory, the effects of beneficial mutations are exponentially distributed where the fitness of the wild type is moderate to high. However, when the fitness of the wild type is low, the data no longer follow an exponential distribution, because many beneficial mutations have large effects on fitness. There is no existing population genetic theory to explain this bias towards mutations of large effects, but it can be readily explained by the underlying biochemistry of rifampicin–RNA polymerase interactions. These results demonstrate the limitations of current population genetic theory for predicting adaptation to severe sources of stress, such as antibiotics, and they highlight the utility of integrating statistical and biophysical approaches to adaptation.     

Competition among plants: Concepts, individual-based modelling approaches, and a proposal for a future research strategy

Competition is a key process in plant populations and communities. We thus need, if we are to predict the responses of ecological systems to environmental change, a comprehensive and mechanistic understanding of plant competition. Considering competition, however, only at the population level is not sufficient because plant individuals usually are different, interact locally, and can adapt their behaviour to the current state of themselves and of their biotic and abiotic environment. Therefore, simulation models that are individual-based and spatially explicit are increasingly used for studying competition in plant systems. Many different individual-based modelling approaches exist to represent competition, but it is not clear how good they are in reflecting essential aspects of plant competition. We therefore first summarize current concepts and theories addressing plant competition. Then, we review individual-based approaches for modelling competition among plants. We distinguish between approaches that are used for more than 10 years and more recent ones. We identify three major gaps that need to be addressed more in the future: the effects of plants on their local environment, adaptive behaviour, and below-ground competition. To fill these gaps, the representation of plants and their interactions have to be more mechanistic than most existing approaches. Developing such new approaches is a challenge because they are likely to be more complex and to require more detailed knowledge and data on individual-level processes underlying competition. We thus need a more integrated research strategy for the future, where empirical and theoretical ecologists as well as computer scientists work together on formulating, implementing, parameterization, testing, comparing, and selecting the new approaches.     

Head and neck lymphatic tumors and bony abnormalities: a clinical and molecular review

Lymphatic malformations and lymphatic-derived tumors commonly involve the head and neck, where they may be associated with bony abnormalities and other systemic symptoms. The reasons for the association between these disorders and local skeletal changes are largely unknown, but such changes may cause significant disease-related morbidity. Ongoing work in molecular and developmental biology is beginning to uncover potential reasons for the bony abnormalities found in head and neck lymphatic disease; this article summarizes current knowledge on possible mechanisms underlying this association.     

Environmental correlates of anuran beta diversity in the Brazilian Cerrado

Evolutionary processes are known to influence contemporary patterns of biological diversity, yet disentangling the effects of current and historical drivers of biodiversity patterns remain challenging. We use spatial analyses of community dissimilarity to generate hypotheses about the current and historical processes underlying patterns of beta diversity in anuran species in the Brazilian Cerrado. Specifically, we use a generalized dissimilarity modeling (GDM) approach to model compositional dissimilarity of anuran species and endemics as a function of geographic separation and local (within‐Cerrado) environmental conditions. To gain insight about potential historical processes, we incorporate information from biomes adjacent to the Cerrado to investigate whether environmental conditions in neighboring areas can help explain patterns of beta diversity within the Cerrado. Patterns of anuran beta diversity of both endemics and all species in the Cerrado appear to be strongly influenced by local environmental gradients, with elevation as one of the most important variables in all models. However, in models using endemic species only, environmental conditions of adjacent biomes were related to beta‐diversity patterns, and more strongly so, than to total species models. These results suggest that phylogenetic niche conservatism within species groups that invaded the Cerrado from adjacent biomes may cause these species to be restricted to environmental conditions within the Cerrado that are most similar to the conditions in the adjacent biome where they originated. Time‐calibrated phylogenies of Cerrado endemics and studies of ancestral and current ranges of Cerrado species are needed to test this hypothesis.     

Dynamics of Membrane Tethers Reveal Novel Aspects of Cytoskeleton-Membrane Interactions in Axons

Mechanical properties of cell membranes are known to be significantly influenced by the underlying cortical cytoskeleton. The technique of pulling membrane tethers from cells is one of the most effective ways of studying the membrane mechanics and the membrane-cortex interaction. In this article, we show that axon membranes make an interesting system to explore as they exhibit both free membrane-like behavior where the tether-membrane junction is movable on the surface of the axons (unlike many other cell membranes) as well as cell-like behavior where there are transient and spontaneous eruptions in the tether force that vanish when F-actin is depolymerized. We analyze the passive and spontaneous responses of axonal membrane tethers and propose theoretical models to explain the observed behavior.     

Intestinal stem cell,muscular niche and Wingless signaling

Stem cells are typically supported by local tissue microenvironment named niche. Intestinal stem cells (ISCs) in the Drosophila midgut do not seem to be typical: they are scattered along the basement membrane composed of extracellular matrix, and are not associated with any obvious cellular niches. In addition, regulatory mechanisms controlling ISC self-renewal remain unknown. Recently, we have obtained evidence to show that Wingless signaling is critical for ISC self-renewal. Wingless is specifically produced from the underlying circular muscles and is able to transverse through the basement membrane and reach ISCs, where it activates a canonical Wnt signaling pathway to promote ISC self-renewal. Our study reveals a muscular niche for ISCs and Wnt signaling as a conserved mechanism regulating ISC self-renewal from Drosophila to mammals. Here we provide a brief overview of our findings, and discuss future perspectives on the regulatory mechanisms underlying ISC self-renewal and differentiation.     

The absence of fire can cause a lag phase: The invasion dynamics of Banksia ericifolia (Proteaceae)

The transition from a species introduction to an invasion often spans many decades (a lag phase). However, few studies have determined the mechanisms underlying lag phases. Such a mechanistic understanding is vital if the potential ecosystem‐level impacts are to be predicted and the invasion risks to be managed proactively. Here we examine Banksia ericifolia, introduced for floriculture to South Africa, as a case study. We found 18 sites where the species has been planted, with self‐sustaining (naturalized) populations at four sites, and an invasive population at one site. The invasion originated from around 100 individuals planted 35 years ago; after several fires this population has grown to approximately 10 000 plants covering about 127 ha. The current invasion of B. ericifolia already has ecosystem‐level impacts, for example the nectar available to bird pollinators has more than doubled, potentially disrupting native pollination networks. If fires occurred at the other naturalized sites we anticipate populations would rapidly spread and densify with invaded areas ultimately become banksia‐dominated woodlands. Indeed the only site other than the invasive site where fire has occurred regularly is already showing signs of rapid population growth and spread. However, recruitment is mainly immediately post fire and no seed bank accumulates in the soil, mechanical control of adult plants is cheap and effective, and immature plants are easily detected. This study is a first in illustrating the importance of fire in driving lag phases and provides a valuable example for why it is essential to determine the mechanisms that mediate lag phases in introduced plant species. Serotinous species that have been introduced to areas where fire is suppressed could easily be misinterpreted as low risk species whilst they remain in a lag phase, but they can represent a major invasion risk.     

Hand-eye coordination during sequential tasks.

The small angle subtended by the human fovea places a premium on the ability to quickly and accurately direct the gaze to targets of interest. Thus the resultant saccadic eye fixations are a very instructive behaviour, revealing much about the underlying cognitive mechanisms that guide them. Of particular interest are the eye fixations used in hand-eye coordination. Such coordination has been extensively studied for single movements from a source location to a target location. In contrast, we have studied multiple fixations where the sources and targets are a function of a task and chosen dynamically by the subject according to task requirements. The task chosen is a copying task: subjects must copy a figure made up of contiguous coloured blocks as fast as possible. The main observation is that although eye fixations are used for the terminal phase of hand movements, they are used for other tasks before and after that phase. The analysis of the spatial and temporal details of these fixations suggests that the underlying decision process that moves the eyes leaves key decisions until just before they are required.     

Background sodium current stabilizes bursting in respiratory pacemaker neurons

Endogenous pacemaker properties have been proposed to generate rhythmic activity underlying many behaviors including respiration. For pacemakers to generate regenerative bursting, background currents maintain their membrane potential (Vm) within a range where bi-stable properties are expressed, thereby stabilizing rhythmogenesis. We previously found that the baseline Vm of respiratory pacemakers is stabilized against hyperpolarizing shifts in their Vm. In response to prolonged hyperpolarizing current injection synaptically isolated respiratory pacemakers steadily depolarize and resume bursting, suggesting a stabilizing background current is involved. What is the ionic basis of this background current in respiratory pacemakers? Here we demonstrate that in low-[Na(+)](o) ACSF, synaptically isolated respiratory pacemakers hyperpolarized and remained outside the bursting window, but could burst upon depolarizing current injection. These data suggest that pacemakers possess a background sodium current that is necessary to bring their Vm into a bursting range. Low-[Na(+)](o) ACSF also abolished the depolarizing shift evoked during prolonged hyperpolarizing current injection, and bursting did not resume. This depolarizing shift persisted in the presence of I(h)-current blockers, but was abolished in tetrodotoxin. Although, under control conditions, the Vm of synaptically isolated respiratory pacemaker neurons was not significantly affected when [K(+)](o) was changed from 3 to 8 mM, the Vm is altered when [K(+)](o) was raised in low-[Na(+)](o) ACSF. Thus, current-clamp studies suggest that respiratory pacemaker neurons possess a background sodium current that maintains their membrane potential within a range where they express bursting, thereby stabilizing rhythmogenesis.     

How environment geometry affects grid cell symmetry and what we can learn from it

The mammalian hippocampal formation provides neuronal representations of environmental location but the underlying mechanisms are unclear. The majority of cells in medial entorhinal cortex and parasubiculum show spatially periodic firing patterns. Grid cells exhibit hexagonal symmetry and form an important subset of this more general class. Occasional changes between hexagonal and non-hexagonal firing patterns imply a common underlying mechanism. Importantly, the symmetrical properties are strongly affected by the geometry of the environment. Here, we introduce a field–boundary interaction model where we demonstrate that the grid cell pattern can be formed from competing place-like and boundary inputs. We show that the modelling results can accurately capture our current experimental observations.     

Modeling trap-awareness and related phenomena in capture-recapture studies

Trap-awareness and related phenomena whereby successive capture events are not independent is a feature of the majority of capture-recapture studies. This phenomenon was up to now difficult to incorporate in open population models and most authors have chosen to neglect it although this may have damaging consequences. Focusing on the situation where animals exhibit a trap response at the occasion immediately following one where they have been trapped but revert to their original naïve state if they are missed once, we show that trap-dependence is more naturally viewed as a state transition and is amenable to the current models of capture-recapture. This approach has the potential to accommodate lasting or progressively waning trap effects.     

Principal stratification in causal inference

Many scientific problems require that treatment comparisons be adjusted for posttreatment variables, but the estimands underlying standard methods are not causal effects. To address this deficiency, we propose a general framework for comparing treatments adjusting for posttreatment variables that yields principal effects based on principal stratification. Principal stratification with respect to a posttreatment variable is a cross-classification of subjects defined by the joint potential values of that posttreatment variable tinder each of the treatments being compared. Principal effects are causal effects within a principal stratum. The key property of principal strata is that they are not affected by treatment assignment and therefore can be used just as any pretreatment covariate. such as age category. As a result, the central property of our principal effects is that they are always causal effects and do not suffer from the complications of standard posttreatment-adjusted estimands. We discuss briefly that such principal causal effects are the link between three recent applications with adjustment for posttreatment variables: (i) treatment noncompliance, (ii) missing outcomes (dropout) following treatment noncompliance. and (iii) censoring by death. We then attack the problem of surrogate or biomarker endpoints, where we show, using principal causal effects, that all current definitions of surrogacy, even when perfectly true, do not generally have the desired interpretation as causal effects of treatment on outcome. We go on to forrmulate estimands based on principal stratification and principal causal effects and show their superiority.     

Desire,Envy and Punishment: A Matsigenka Emotion Schema in Illness Narratives and Folk Stories

Accumulating evidence suggests that folktales in some societies are characterized by a culturally constructed underlying emotional structure, or Cultural Emotion Schema. In this paper we argue that Matsigenka illness narratives and folk stories share an underlying emotion schema, in which death and suffering result from conflicts between strong-willed individuals prompting anger and aggression. Analysis of illness narratives collected by Izquierdo in the Matsigenka community of Kamisea in the Peruvian Amazon between 1996 and 1999 reveals a common pattern in which envy and frustration lead to the belief in sorcery as the main cause of illness and death. This pattern contrasts with the typical stories of a previous generation collected by the Johnsons among the Matsigenka of Shimaa and other Matsigenka researchers, where sorcery beliefs were virtually absent. Our argument is that important changes in ecology, community, politics, and religion have led to a systematic rise in feelings of envy and frustration, and that these have increased the likelihood that sorcery accusations will occur. We explore the likelihood that such beliefs increase as egalitarian peoples become more crowded into settlements where they are likely to experience greater inequality, more competition for resources and increased societal and personal stress.     

The fungal pattern recognition receptor, Dectin-1, and the associated cluster of C-type lectin-like receptors

The mammalian natural killer gene complex (NKC) contains several families of type II transmembrane C-type lectin-like receptors (CLRs) that are best known for their involvement in the detection of virally infected or transformed cells, through the recognition of endogenous (or self) proteinacious ligands. However, certain CLR families within the NKC, particularly those expressed by myeloid cells, recognize structurally diverse ligands and perform a variety of other immune and homoeostatic functions. One such family is the 'Dectin-1 cluster' of CLRs, which includes MICL, CLEC-2, CLEC12B, CLEC9A, CLEC-1, Dectin-1 and LOX-1. Here, we review each of these CLRs, exploring our current understanding of their ligands and functions and highlighting where they have provided new insights into the underlying mechanisms of immunity and homeostasis.     

Anopheles gambiae innate immunity

The successful development of Plasmodium in Anopheles mosquitoes is governed by complex molecular and cellular interactions that we are just beginning to understand. Anopheles immune system has received particular attention as genetic evidence points clearly to its critical role in eliminating the majority of parasites invading the midgut epithelium. Several factors regulating Plasmodium development have been identified and tentatively assigned to the individual steps leading to mosquito immune reactions; non-self-recognition, signal modulation, signal transduction and effector mechanisms. Detailed knowledge of these steps and their underlying molecular mechanisms may offer novel perspectives to abort Plasmodium development in the vector. Here, we summarize our current knowledge of mosquito innate immunity highlighting both, recent advances and areas where additional research is required.     

DPP6 establishes the A-type K(+) current gradient critical for the regulation of dendritic excitability in CA1 hippocampal neurons

Subthreshold-activating A-type K(+) currents are essential for the proper functioning of the brain, where they act to delay excitation and regulate firing frequency. In CA1 hippocampal pyramidal neuron dendrites, the density of A-type K(+) current increases with distance from the soma, playing an important role in synaptic integration and plasticity. The mechanism underlying this gradient has, however, remained elusive. Here, dendritic recordings from mice lacking the Kv4 transmembrane auxiliary subunit DPP6 revealed that this protein is critical for generating the A-current gradient. Loss of DPP6 led to a decrease in A-type current, specifically in distal dendrites. Decreased current density was accompanied by a depolarizing shift in the voltage dependence of channel activation. Together these changes resulted in hyperexcitable dendrites with enhanced dendritic AP back-propagation, calcium electrogenesis, and induction of synaptic long-term potentiation. Despite enhanced dendritic excitability, firing behavior evoked by somatic current injection was mainly unaffected in DPP6-KO recordings, indicating compartmentalized regulation of neuronal excitability.