Fluorescent protein-based technologies: shedding new light on the plant endomembrane system

Without doubt, GFP and spectral derivatives have revolutionized the way biologists approach their journey toward the discovery of how plant cells function. It is fascinating that in its early days GFP was used merely for localization studies, but as time progressed researchers successfully explored new avenues to push the power of GFP technology to reach new and exciting research frontiers. This has had a profound impact on the way we can now study complex and dynamic systems such as plant endomembranes. Here we briefly describe some of the approaches where GFP has revolutionized in vivo studies of protein distribution and dynamics and focus on two emerging approaches for the application of GFP technology in plant endomembranes, namely optical tweezers and forward genetics approaches, which are based either on the light or on genetic manipulation of secretory organelles to gain insights on the factors that control their activities and integrity.     

Fostering Industrial Symbiosis With Agent-Based Simulation and Participatory Modeling

The sciences of industrial ecology, complex systems, and adaptive management are intimately related, since they deal with flows and dynamic interdependencies between system elements of various kinds. As such, the tool kit of complex systems science could enrich our understanding of how industrial ecosystems might evolve over time. In this article, I illustrate how an important tool of complex systems science— agent-based simulation —can help to identify those potential elements of an industrial ecosystem that could work together to achieve more eco-efficient outcomes. For example, I show how agent-based simulation can generate cost-efficient energy futures in which groups of firms behave more eco-efficiently by introducing strategically located clusters of renewable, low-emissions, distributed generation. I then explain how role-playing games and participatory modeling can build trust and reduce conflict about the sharing of common-pool resources such as water and energy among small clusters of evolving agents. Collective learning can encourage potential industrial partners to gradually cooperate by exchanging by-products and/or sharing common infrastructure by dint of their close proximity. This kind of coevolutionary learning, aided by participatory modeling, could help to bring about industrial symbiosis.     

Catabolism of dimethylsulphoniopropionate: microorganisms, enzymes and genes

The compatible solute dimethylsulphoniopropionate (DMSP) has important roles in marine environments. It is an anti-stress compound made by many single-celled plankton, some seaweeds and a few land plants that live by the shore. Furthermore, in the oceans it is a major source of carbon and sulphur for marine bacteria that break it down to products such as dimethyl sulphide, which are important in their own right and have wide-ranging effects, from altering animal behaviour to seeding cloud formation. In this Review, we describe how recent genetic and genomic work on the ways in which several different bacteria, and some fungi, catabolize DMSP has provided new and surprising insights into the mechanisms, regulation and possible evolution of DMSP catabolism in microorganisms.     

Host selection in insects: reproductive interference shapes behavior of ovipositing females

In nature, closely related species often utilize different host species, but it is still unclear what factors contribute to the evolution and maintenance of such diversified host selection. In this review, I describe how negative interspecific mating interactions (reproductive interference) can shape host selection by animals, focusing mainly on phytophagous and predatory insects. First, I explain an important premise of this hypothesis, which is that the adult reproductive site is the same as the feeding site for the offspring. Next, I describe several mathematical models and well-studied empirical systems to show that reproductive interference can sufficiently drive and maintain different host selection between phylogenetically related species. Then, I argue for the first time that reproductive interference can cause an oviposition preference in insects that is not optimal for the survival and development of the offspring, as a result of maternal adaptive behavior that maximizes the mother's own fitness. Furthermore, I argue that in insects, reproductive interference probably shapes oviposition behavior before the female alights on the host (e.g., habitat preference), without affecting post-alighting decision making. I would like to emphasize that these two arguments represent the novel approach to clarify the unrevealed pattern of complex insect oviposition behavior.     

The Costs of Mutualism

Mutualisms are of central importance in biological systems.Despite growing attention in recent years, however, few conceptualthemes have yet to be identified that span mutualisms differingin natural history. Here I examine the idea that the ecologyand evolution of mutualisms are shaped by diverse costs, notonly by the benefits they confer. This concept helps link mutualismto antagonisms such as herbivory, predation, and parasitism,interactions defined largely by the existence of costs. I firstbriefly review the range of costs associated with mutualisms,then describe how one cost, the consumption of seeds by pollinatoroffspring, was quantified for one fig/pollinator mutualism.I compare this cost to published values for other fig/pollinatormutualisms and for other kinds of pollinating seed parasitemutualisms, notably the yucca/yucca moth interaction. I thendiscuss four issues that fundamentally complicate comparativestudies of the cost of mutualism: problems of knowing how tomeasure the magnitude of any one cost accurately; problems associatedwith using average estimates in the absence of data on sourcesof variation; complications arising from the complex correlatesof costs, such as functional linkages between costs and benefits;and problems that arise from considering the cost of mutualismas a unilateral issue in what is fundamentally a reciprocalinteraction. The rich diversity of as-yet unaddressed questionssurrounding the costs of mutualism may best be investigatedvia detailed studies of individual interactions.     

An Efficient, Nonlinear Stability Analysis for Detecting Pattern Formation in Reaction Diffusion Systems

Reaction diffusion systems are often used to study pattern formation in biological systems. However, most methods for understanding their behavior are challenging and can rarely be applied to complex systems common in biological applications. I present a relatively simple and efficient, nonlinear stability technique that greatly aids such analysis when rates of diffusion are substantially different. This technique reduces a system of reaction diffusion equations to a system of ordinary differential equations tracking the evolution of a large amplitude, spatially localized perturbation of a homogeneous steady state. Stability properties of this system, determined using standard bifurcation techniques and software, describe both linear and nonlinear patterning regimes of the reaction diffusion system. I describe the class of systems this method can be applied to and demonstrate its application. Analysis of Schnakenberg and substrate inhibition models is performed to demonstrate the methods capabilities in simplified settings and show that even these simple models have nonlinear patterning regimes not previously detected. The real power of this technique, however, is its simplicity and applicability to larger complex systems where other nonlinear methods become intractable. This is demonstrated through analysis of a chemotaxis regulatory network comprised of interacting proteins and phospholipids. In each case, predictions of this method are verified against results of numerical simulation, linear stability, asymptotic, and/or full PDE bifurcation analyses.     

Hunting G-quadruplexes

Whilst DNA spends much of its time in the double-stranded form, frequently in storage, wrapped around histones and packaged as chromatin, it can also form other complex structures, which may play a role in natural regulation and gene control. These alternative structures therefore also present an interesting novel series of targets for artificial intervention, and so may lead to novel therapeutics. In this review, I describe the current understanding of how genomic and bioinformatics studies may be used to understand the roles that one such structure, the four-stranded guanine-rich G-quadruplex, may play in the genome, and outline how these may be considered as targets for intervention. I will also describe recent work looking at RNA G-quadruplexes, and the biological roles they may play.     

Onward from the cradle

This essay records a voyage of discovery from the “cradle of cell biology” to the present, focused on the biology of the oldest known cell organelle, the cilium. In the “romper room” of cilia and microtubule (MT) biology, the sliding MT hypothesis of ciliary motility was born. From the “summer of love,” students and colleagues joined the journey to test switch-point mechanisms of motility. In the new century, interest in nonmotile (primary) cilia, never lost from the cradle, was rekindled, leading to discoveries relating ciliogenesis to autophagy and hypotheses of how molecules cross ciliary necklace barriers for cell signaling.     

Emergent Systems Energy Laws for Predicting Myosin Ensemble Processivity

In complex systems with stochastic components, systems laws often emerge that describe higher level behavior regardless of lower level component configurations. In this paper, emergent laws for describing mechanochemical systems are investigated for processive myosin-actin motility systems. On the basis of prior experimental evidence that longer processive lifetimes are enabled by larger myosin ensembles, it is hypothesized that emergent scaling laws could coincide with myosin-actin contact probability or system energy consumption. Because processivity is difficult to predict analytically and measure experimentally, agent-based computational techniques are developed to simulate processive myosin ensembles and produce novel processive lifetime measurements. It is demonstrated that only systems energy relationships hold regardless of isoform configurations or ensemble size, and a unified expression for predicting processive lifetime is revealed. The finding of such laws provides insight for how patterns emerge in stochastic mechanochemical systems, while also informing understanding and engineering of complex biological systems.     

Invertebrate central pattern generator circuits

There are now a reasonable number of invertebrate central pattern generator (CPG) circuits described in sufficient detail that a mechanistic explanation of how they work is possible. These small circuits represent the best-understood neural circuits with which to investigate how cell-to-cell synaptic connections and individual channel conductances combine to generate rhythmic and patterned output. In this review, some of the main lessons that have appeared from this analysis are discussed and concrete examples of circuits ranging from single phase to multiple phase patterns are described. While it is clear that the cellular components of any CPG are basically the same, the topology of the circuits have evolved independently to meet the particular motor requirements of each individual organism and only a few general principles of circuit operation have emerged. The principal usefulness of small systems in relation to the brain is to demonstrate in detail how cellular infrastructure can be used to generate rhythmicity and form specialized patterns in a way that may suggest how similar processes might occur in more complex systems. But some of the problems and challenges associated with applying data from invertebrate preparations to the brain are also discussed. Finally, I discuss why it is useful to have well-defined circuits with which to examine various computational models that can be validated experimentally and possibly applied to brain circuits when the details of such circuits become available.     

Are island‐like systems biologically similar to islands? A review of the evidence

Islands are geographically defined as land masses completely surrounded by water, and island systems have been used as models for many biogeographic, ecological, and evolutionary theories ever since Darwin's pioneering efforts. However, their biological definition is complex. Over the past few decades these theories have been applied to many study systems that only share some geographic features with island systems. These features include spatial fragmentation, limited area, spatial and temporal isolation from adjacent parts of the system, and low connectivity between different parts within the system, to mention just a few. These systems vary in their form, the matrix that surrounds them, the factors defining their borders, the extent of insularity they impose on the different taxa, and their geological similarity to different types of actual islands. Here, I seek to understand whether such island‐like systems (ILS) function biologically as true islands. In the first part, I describe the wide diversity of ILS suggested in the literature and the variation in the features that define their insularity. In the second part, I review the extent to which the main theories of island biology are applicable to these systems: species–area and species–isolation relationships, community composition, evolutionary radiations, and the extent of endemism and genetic diversity. In the third and final part, I suggest a new conceptual framework within which to classify and study the biology of ILS, as well as practical future research directions. I conclude that the term ‘biological island’ is a multi‐faceted concept, loosely related to its geographical definition. As ILS are often less isolated than true islands, and their biological patterns are only partly similar to those of true islands (and even this is true only for some ILS) the use of the term ‘island’ to describe any isolated habitat is therefore inappropriate.     

Secular citizenship and Muslim belonging in Turkey: migrant perspectives

In recent years, academic critique has worked toward exposing the underlying ethno-religious biases in official formulations of secular citizenship in Turkey. While such studies have highlighted the contradictions and inconsistencies that emerge in these grand narratives of national belonging, they have tended to privilege statist determinants of the bounds of nationhood. In this article, I offer an intervention into this discussion by exploring how citizens themselves encounter and embrace religion as a marker of national belonging in Turkey. In particular, I discuss the case of the 1950s Bosniak migration to Turkey and explore the salience of the migratory journey in informing their experiences of secular citizenship and national belonging.     

Eukaryotic complex I: functional diversity and experimental systems to unravel the assembly process

With more than 40 subunits, one FMN co-factor and eight FeS clusters, complex I or NADH:ubiquinone oxidoreductase is the largest multimeric respiratory enzyme in the mitochondria. In this review, we focus on the diversity of eukaryotic complex I. We describe the additional activities that have been reported to be associated with mitochondrial complex I and discuss their physiological significance. The recent identification of complex I-like enzymes in the hydrogenosome, a mitochondria-derived organelle is also discussed here. Complex I assembly in the mitochondrial inner membrane is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes. The most prevalent forms of mitochondrial dysfunction in humans are deficiencies in complex I and remarkably, the molecular basis for 60% of complex I-linked defects is currently unknown. This suggests that mutations in yet-to-be-discovered assembly genes should exist. We review the different experimental systems for the study of complex I assembly. To our knowledge, in none of them, large screenings of complex I mutants have been performed. We propose that the unicellular green alga Chlamydomonas reinhardtii is a promising system for such a study. Complex I mutants can be easily scored on a phenotypical basis and a large number of transformants generated by insertional mutagenesis can be screened, which opens the possibility to find new genes involved in the assembly of the enzyme. Moreover, mitochondrial transformation, a recent technological advance, is now available, allowing the manipulation of all five complex I mitochondrial genes in this organism.     

A Developmental Journey and Lessons Learned Along the Way

A career in science is a journey of wonder and discovery. To succeed in science requires curiosity, perseverance, a good dose of luck, and wise guidance from those who have taken the journey ahead of you. We also need to use our science skills to contribute to public debate on complex issues of the day.Being honored by the 2009 American Society for Cell Biology Women in Cell Biology (WICB) Senior Award has provided me with an opportunity to look back and examine the importance of mentorship and role models, both female and male, in my career. I am fundamentally a basic biologist, driven by my curiosity about how the world works. The question that has fascinated me for over 30 years is one that we can all relate to: How is it that complex, rational organisms such as ourselves can arise from a single cell, the size of a speck of dust?Over the years my lab colleagues and I have explored many aspects of that question, using mice as our model system, and we''ve discovered more and more about the hierarchy of cell decisions that begins when sperm hits egg. Along the way we have contributed to the development of techniques for manipulating the mouse genome, helped identify key signaling pathways that control blood vessel development, and isolated novel stem cells from the mouse blastocyst. But I always return to the fundamental questions of lineage development in the early embryo, attacking the problem with new tools as they become available.     

Sweet host revenge: Galectins and GBPs join forces at broken membranes

Most bacterial pathogens enter and exit eukaryotic cells during their journey through the vertebrate host. In order to endure inside a eukaryotic cell, bacterial invaders commonly employ bacterial secretion systems to inject host cells with virulence factors that co‐opt the host's membrane trafficking systems and thereby establish specialised pathogen‐containing vacuoles (PVs) as intracellular niches permissive for microbial growth and survival. To defend against these microbial adversaries hiding inside PVs, host organisms including humans evolved an elaborate cell‐intrinsic armoury of antimicrobial weapons that include noxious gases, antimicrobial peptides, degradative enzymes, and pore‐forming proteins. This impressive defence machinery needs to be accurately delivered to PVs, in order to fight off vacuole‐dwelling pathogens. Here, I discuss recent evidence that the presence of bacterial secretion systems at PVs and the associated destabilisation of PV membranes attract such antimicrobial delivery systems consisting of sugar‐binding galectins as well as dynamin‐like guanylate‐binding proteins (GBPs). I will review recent advances in our understanding of intracellular immune recognition of PVs by galectins and GBPs, discuss how galectins and GBPs control host defence, and highlight important avenues of future research in this exciting area of cell‐autonomous immunity.     

A path to the powerhouse: systems‐to‐structure approaches for studying mitochondrial proteins

The young investigator award from the Protein Society was a special honor for me because, at its essence, the goal of my laboratory is to define what obscure proteins do. Years ago, I stumbled into mitochondria as a venue for this work, and these organelles continue to define the biological theme of my laboratory. Our approaches are fairly broad, reflecting my own somewhat unorthodox training among diverse scientific fields spanning organic synthesis, chemical biology, mechanistic biochemistry, signal transduction, and systems biology. Yet, whatever the theme or the discipline, we aim to understand how proteins work—especially those that hide in the dark corners of mitochondria. Below, I recount my own path into this arena of protein science, and describe how my experiences along the way have shaped our current multi‐disciplinary efforts to define the inner workings of this complex biological system.     

The behavioural ecology of marine cleaning mutualisms

Cleaning interactions, in which a small ‘cleaner’ organism removes and often consumes material from a larger ‘client’, are some of the most enigmatic and intriguing of interspecies interactions. Early research on cleaning interactions canonized the view that they are mutualistic, with clients benefiting from parasite removal and cleaners benefiting from a meal, but subsequent decades of research have revealed that the dynamics of these interactions can be highly complex. Despite decades of research on marine cleaning interactions (the best studied cleaning systems), key questions remain, including how the outcome of an individual cleaning interaction depends on ecological, behavioural, and social context, how such interactions arise, and how they remain stable over time. Recently, studies of marine parasites, long-term data from coral reef communities with and without cleaners, increased behavioural observations recorded using remote video, and a focus on a larger numbers of cleaning species have helped bring about key conceptual advances in our understanding of cleaning interactions. In particular, evidence now suggests that the ecological, behavioural, and social contexts of a given cleaning interaction can result in the outcome ranging from mutualistic to parasitic, and that cleaning interactions are mediated by signals that can also vary with context. Signals are an important means by which animals extract information about one another, and thus represent a mechanism by which interspecific partners can determine when, how, and with whom to interact. Here, I review our understanding of the behavioural ecology of marine cleaning interactions. In particular, I argue that signals provide a useful framework for advancing our understanding of several important outstanding questions. I discuss the costs and benefits of cleaning interactions, review how cleaners and clients recognize and assess one another using signals, and discuss how signal reliability, or ‘honesty’, may be maintained in cleaning systems. Lastly, I discuss the sensory ecology of both cleaners and clients to highlight what marine cleaning systems can tell us about signalling behaviour, signal form, and signal evolution in a system where signals are aimed at multiple receiver species. Overall, I argue that future research on cleaning interactions has much to gain by continuing to shift the research focus toward examining the variable outcomes of cleaning interactions in relation to the broader behavioural, social, and ecological contexts.     

Many little things: one geneticist's view of complex diseases

Gene targeting is commonly used to knock out genes in order to understand their function. It has also been used successfully to model the relatively rare human genetic diseases that are caused by homozygous loss of gene function. Modelling the much more common multifactorial diseases that have strong genetic and environmental causes is less easy. Here, I describe my personal voyage into this challenging field, using gene targeting to alter the expression of genes that impact on hypertension and diabetes.     

ER-mediated phagocytosis: a new membrane for new functions

Genomics and other high-throughput approaches, such as proteomics, are changing the way we study complex biological systems. In the past few years, these approaches have contributed markedly to improving our understanding of phagocytosis. Indeed, the ability to study biological systems by monitoring hundreds of proteins provides a level of resolution that is not attainable by the usual 'one protein at a time' approach. In this article, I discuss how proteomic approaches have revealed surprising findings that enable us to revisit established concepts, such as the origin of the phagosome membrane, and to propose new models of cell organization and the link between innate and adaptive immunity.