New approaches to the problem of generating coherent,reproducible phenotypes

Fundamental, unresolved questions in biology include how a bacterium generates coherent phenotypes, how a population of bacteria generates a coherent set of such phenotypes, how the cell cycle is regulated and how life arose. To try to help answer these questions, we have developed the concepts of hyperstructures, competitive coherence and life on the scales of equilibria. Hyperstructures are large assemblies of macromolecules that perform functions. Competitive coherence describes the way in which organisations such as cells select a subset of their constituents to be active in determining their behaviour; this selection results from a competition between a process that is responsible for a historical coherence and another process responsible for coherence with the current environment. Life on the scales of equilibria describes how bacteria depend on the cell cycle to negotiate phenotype space and, in particular, to satisfy the conflicting constraints of having to grow in favourable conditions so as to reproduce yet not grow in hostile conditions so as to survive. Both competitive coherence and life on the scales deal with the problem of reconciling conflicting constraints. Here, we bring together these concepts in the common framework of hyperstructures and make predictions that may be tested using a learning program, Coco, and secondary ion mass spectrometry.     

Hypercomplexity

What is biological complexity? How many sorts exist? Are there levels of complexity? How are they related to one another? How is complexity related to the emergence of new phenotypes? To try to get to grips with these questions, we consider the archetype of a complex biological system, Escherichia coli. We take the position that E. coli has been selected to survive adverse conditions and to grow in favourable ones and that many other complex systems undergo similar selection. We invoke the concept of hyperstructures which constitute a level of organisation intermediate between macromolecules and cells. We also invoke a new concept, competitive coherence, to describe how phenotypes are created by a competition between maintaining a consistent story over time and creating a response that is coherent with respect to both internal and external conditions. We suggest how these concepts lead to parameters suitable for describing the rich form of complexity termed hypercomplexity and we propose a relationship between competitive coherence and emergence.     

Effects of plant species and soil history on root morphology,arbuscular mycorrhizal colonization of roots,and biomass in four tallgrass prairie species

Although dominant C₄ grasses in tallgrass prairie are highly mycotrophic, for many non-dominant species neither extent of mycorrhizal colonization nor root morphology effects on plant–soil feedback interactions are known. In a laboratory study conducted from November 2013 to February 2014 at Governors State University (University Park, IL), we grew plants of a dominant C₄ grass (Andropogon gerardii) and three non-dominant forbs (Symphyotrichum laeve var. laeve, Symphyotrichum novae-angliae and Parthenium integrifolium) individually in soil collected in the field beneath a conspecific, collected beneath another study species, or in sterilized soil. The study addressed the following questions: (1) Is extent of mycorrhizal colonization of roots related to root structure? (2) How does soil history interact with plant root traits to influence plant–soil feedback? (3) How might plant–soil feedback patterns influence competitive interactions among study species? We found that proportion arbuscular mycorrhizal fungi (AMF) colonization decreased with increasing specific root length. Soil history had a stronger influence than plant species on total biomass of plants, with all species having highest total biomass when grown in Andropogon soil. Consequently, net, or heterospecific, feedback did not differ among pairwise species combinations, and was not different from 0. While these results suggest that no study species should have a competitive advantage in the field, Andropogon might still have an advantage through mechanisms such as competition for light. Future work in the field and including less mycotrophic species is needed to better understand AMF effects on competitive interactions.

     

Fifteen compelling open questions in plant cell biology

As scientists, we are at least as excited about the open questions—the things we do not know—as the discoveries. Here, we asked 15 experts to describe the most compelling open questions in plant cell biology. These are their questions: How are organelle identity, domains, and boundaries maintained under the continuous flux of vesicle trafficking and membrane remodeling? Is the plant cortical microtubule cytoskeleton a mechanosensory apparatus? How are the cellular pathways of cell wall synthesis, assembly, modification, and integrity sensing linked in plants? Why do plasmodesmata open and close? Is there retrograde signaling from vacuoles to the nucleus? How do root cells accommodate fungal endosymbionts? What is the role of cell edges in plant morphogenesis? How is the cell division site determined? What are the emergent effects of polyploidy on the biology of the cell, and how are any such “rules” conditioned by cell type? Can mechanical forces trigger new cell fates in plants? How does a single differentiated somatic cell reprogram and gain pluripotency? How does polarity develop de-novo in isolated plant cells? What is the spectrum of cellular functions for membraneless organelles and intrinsically disordered proteins? How do plants deal with internal noise? How does order emerge in cells and propagate to organs and organisms from complex dynamical processes? We hope you find the discussions of these questions thought provoking and inspiring.

We asked 15 experts to address what they consider to be the most compelling open questions in plant cell biology and these are their questions.     

Root dynamics and global change: seeking an ecosystem perspective

Changes in the production and turnover of roots in forests and grasslands in response to rising atmospheric CO₂ concentrations, elevated temperatures, altered precipitation, or nitrogen deposition could be a key link between plant responses and longer-term changes in soil organic matter and ecosystem carbon balance. Here we summarize the experimental observations, ideas, and new hypotheses developed in this area in the rest of this volume. Three central questions are posed. Do elevated atmospheric CO₂, nitrogen deposition, and climatic change alter the dynamics of root production and mortality? What are the consequences of root responses to plant physiological processes? What are the implications of root dynamics to soil microbial communities and the fate of carbon in soil? Ecosystem-level observations of root production and mortality in response to global change parameters are just starting to emerge. The challenge to root biologists is to overcome the profound methodological and analytical problems and assemble a more comprehensive data set with sufficient ancillary data that differences between ecosystems can be explained. The assemblage of information reported herein on global patterns of root turnover, basic root biology that controls responses to environmental variables, and new observations of root and associated microbial responses to atmospheric and climatic change helps to sharpen our questions and stimulate new research approaches. New hypotheses have been developed to explain why responses of root turnover might differ in contrasting systems, how carbon allocation to roots is controlled, and how species differences in root chemistry might explain the ultimate fate of carbon in soil. These hypotheses and the enthusiasm for pursuing them are based on the firm belief that a deeper understanding of root dynamics is critical to describing the integrated response of ecosystems to global change.     

Competition and coexistence in plant communities

Few ecologists today doubt that competition is an important structuring factor in plant communities, but researchers disagree on the circumstances where it is most intense, and on which traits can be considered to contribute to competitive ability in different species. The distinction between a species' effect on resources and its response to reduced resource levels might help to solve these questions. Whereas classical competition theory predicts competitive exclusion of species with similar requirements, recent ideas stress that species diversity may be explained by a multitude of processes acting at different scales, and that similarities in competitive abilities often may facilitate coexistence.     

Increased community compositional dissimilarity alleviates species loss following nutrient enrichment at large spatial scales

Aims Anthropogenic activities have drastically increased nutrient availability, resulting in declines in species richness in many plant communities. However, most previous studies have explored only species-loss patterns and mechanisms over small sampling areas, so their results might overestimate species loss at larger spatial scales. The aim of this research was to explore species diversity change patterns and species-loss rates at multiple scales in alpine meadow communities following nutrient enrichment. Specifically, we asked two closely related questions: (i) do changes in species diversity and species-loss patterns differ among spatial scales? and (ii) how does community compositional dissimilarity and species turnover change among spatial scale?     

The importance of importance

Failure to distinguish between 'importance' and 'intensity' of competition has hindered our ability to resolve key questions about the role interactions may play in plant communities. Here we examine how appropriate application of metrics of importance and intensity is integral to investigating key theories in plant community ecology and how ignoring this distinction has lead to confusion and possibly spurious conclusions. We re-explore the relationship between competition intensity and importance for individuals across gradients, and apply our review of concepts to published data to help clarify the debate. We demonstrate that competition importance and intensity need not be correlated and show how explicit application of the intensity and importance of competition may reconcile apparently incompatible paradigms.     

Certified reference materials for the determination of mycotoxins

A continuing fundamental trend in the area of quality assurance in analytical laboratories are measures that enable trace-ability of analytical results to internationally renowned units, like e.g. the mole. Especially certified reference materials (CRMs) are important tools for achieving this goal. What are CRMs? Why do we need them in the field of mycotoxin analysis? Which kind of CRMs are currently available for the determination of mycotoxins and how should they be used? These are questions, which are increasingly being asked. This article attempts to answer these questions.     

Do invasive species show higher phenotypic plasticity than native species and,if so,is it adaptive? A meta‐analysis

Do invasive plant species have greater phenotypic plasticity than non-invasive species? And, if so, how does this affect their fitness relative to native, non-invasive species? What role might this play in plant invasions? To answer these long-standing questions, we conducted a meta-analysis using data from 75 invasive/non-invasive species pairs. Our analysis shows that invasive species demonstrate significantly higher phenotypic plasticity than non-invasive species. To examine the adaptive benefit of this plasticity, we plotted fitness proxies against measures of plasticity in several growth, morphological and physiological traits to test whether greater plasticity is associated with an improvement in estimated fitness. Invasive species were nearly always more plastic in their response to greater resource availability than non-invasives but this plasticity was only sometimes associated with a fitness benefit. Intriguingly, non-invasive species maintained greater fitness homoeostasis when comparing growth between low and average resource availability. Our finding that invasive species are more plastic in a variety of traits but that non-invasive species respond just as well, if not better, when resources are limiting, has interesting implications for predicting responses to global change.     

The method of synthesis in ecology

Synthesis of results from different investigations is an important activity for ecologists but when compared with analysis the method of synthesis has received little attention. Ecologists usually proceed intuitively and this can lead to a problem in defining differences between the syntheses made by different scientists. It also leads to criticism from scientists favoring analytical approaches that the construction of general theory is an activity that does not follow the scientific method. We outline a methodology for scientific inference about integrative concepts and the syntheses made in constructing them and illustrate how this can be applied in the development of general theory from investigations into particular ecological systems. The objective is to construct a causal scientific explanation. This has four characteristics. (1) It defines causal and/or organizational processes that describe how systems function. (2) These processes are consistent – under the same conditions they will produce the same effect. (3) A causal scientific explanation provides general information about events of a similar kind. (4) When experiments are possible then a designed manipulation will produce a predictable response. The essential characteristic of making synthesis to construct a causal scientific explanation is that it is progressive and we judge progress made by assessing the coherence of the explanation using six criteria: acceptability of individual propositions including that they have been tested with data, consistency of concept definitions, consistency in the type of concepts used in making the explanation, that ad hoc propositions are not used, that there is economy in the number of propositions used, that the explanation applies to broad questions. We illustrate development of a causal scientific explanation for the concept of long-lived pioneer tree species, show how the coherence of this explanation can be assessed, and how it could be improved.     

Theoretical analysis of the evolution of immune memory

Background

The ability of an immune system to remember pathogens improves the chance of the host to survive a second exposure to the same pathogen. This immunological memory has evolved in response to the pathogen environment of the hosts. In vertebrates, the memory of previous infection is physiologically accomplished by the development of memory T and B cells. Many questions concerning the generation and maintenance of immunological memory are still debated. Is there a limit to how many memory cells a host can generate and maintain? If there is a limit, how should new cells be incorporated into a filled memory compartment? And how many different pathogens should the immune system remember?

Results

In this study, we examine how memory traits evolve as a response to different pathogen environments using an individual-based model. We find that even without a cost related to the maintenance of a memory pool, the positive effect of bigger memory pool sizes saturates. The optimal diversity of a limited memory pool is determined by the probability of re-infection, rather than by the prevalence of a pathogen in the environment, or the frequency of exposure.

Conclusions

Relating immune memory traits to the pathogen environment of the hosts, our population biological framework sheds light on the evolutionary determinants of immune memory.

     

Mechanical explanation of nature and its limits in Kant's Critique of judgment

In this paper I discuss two questions. What does Kant understand by mechanical explanation in the Critique of judgment? And why does he think that mechanical explanation is the only type of the explanation of nature available to us? According to the interpretation proposed, mechanical explanations in the Critique of judgment refer to a particular species of empirical causal laws. Mechanical laws aim to explain nature by reference to the causal interaction between the forces of the parts of matter and the way in which they form into complex material wholes. Just like any other empirical causal law, however, mechanical laws can never be known with full certainty. The conception according to which we can explain all of nature by means of mechanical laws, it turns out, is based on what Kant calls 'regulative' or 'reflective' considerations about nature. Nothing in Kant's Critique of judgment suggests that these considerations can ever be justified by reference to how the natural world really is. I suggest that what, upon first consideration, appears to be a thoroughly mechanistic conception of nature in Kant is much more limited than one might have expected.     

The impact of global climate change on genetic diversity within populations and species

Genetic diversity provides the basic substrate for evolution, yet few studies assess the impacts of global climate change (GCC) on intraspecific genetic variation. In this review, we highlight the importance of incorporating neutral and non‐neutral genetic diversity when assessing the impacts of GCC, for example, in studies that aim to predict the future distribution and fate of a species or ecological community. Specifically, we address the following questions: Why study the effects of GCC on intraspecific genetic diversity? How does GCC affect genetic diversity? How is the effect of GCC on genetic diversity currently studied? Where is potential for future research? For each of these questions, we provide a general background and highlight case studies across the animal, plant and microbial kingdoms. We further discuss how cryptic diversity can affect GCC assessments, how genetic diversity can be integrated into studies that aim to predict species' responses on GCC and how conservation efforts related to GCC can incorporate and profit from inclusion of genetic diversity assessments. We argue that studying the fate of intraspecifc genetic diversity is an indispensable and logical venture if we are to fully understand the consequences of GCC on biodiversity on all levels.     

Be more specific! Laser-assisted microdissection of plant cells

Laser-assisted microdissection (LAM) is a powerful tool for isolating specific tissues, cell types and even organelles from sectioned biological specimen in a manner conducive to the extraction of RNA, DNA or protein. LAM, which is an established technique in many areas of biology, has now been successfully adapted for use with plant tissues. Here, we provide an overview of the processes involved in conducting a successful LAM study in plants and review recent developments that have made this technique even more desirable. We also discuss how the technology might be exploited to answer some pertinent questions in plant biology.     

How much do phenotypic plasticity and local genetic variation contribute to phenotypic divergences along environmental gradients in widespread invasive plants? A meta‐analysis

For introduced species that have spread across a wide distributional range, phenotypic plasticity (PLA) has often been proposed as an important contributor to invasion success, because it increases the survival rate during initial colonization. In contrast, local genetic variation (LOC) has also been proposed to be important, because it could allow invaders to evolve high performance in a new habitat. While evolutionary ecologists have long been interested in understanding genetic mechanisms that allow rapid colonization and spread of species, until recently experimental tests of these concepts have been limited. As a step towards generalization in our understanding of the importance of PLA and LOC, we review the current state of the literature on this topic using meta‐analysis. Here, we focused on three fundamental questions: 1) which strategy, PLA or LOC, better explains the phenotypic divergences during invader range expansion across different environmental gradients? 2) Which species characteristics correlate with the occurrence of these different phenomena? And 3) does the detection of PLA versus LOC depend on the trait studied? Using meta‐analysis we found that plasticity explained a higher proportion of phenotypic variation regardless of the environmental gradients studied or plant growth forms. PLA predominated in clonal, self‐compatible and perennial species, while LOC predominated in annual species. The patterns were trait‐dependent: LOC was significantly more important than PLA in phenology, while opposite patterns were found in fecundity and biomass allocation. The frequent simultaneous detection of PLA and genotypic variation in PLA among invasive populations suggested that PLA might benefit from LOC to some extent. Our results also indicate that the contribution of plasticity to the competitive advantages of invasive plants may be more informative than the level of plasticity itself. Synthesis For invasive plants that spread across a wide distributional range, understanding the mechanisms that allow rapid colonization and spread is crucial. Phenotypic plasticity (PLA) and local genetic variation (LOC) are both believed to play important roles in promoting range expansion. However, it is not clear which mechanism, PLA or LOC, contributes more to this process. According to our meta–analysis, PLA explained a higher proportion of adaptive phenotypic variation in most cases. Nevertheless, the predominance of an expansion mechanism depends on species characteristics and the trait studied. PLA may benefit from LOC to some extent. We suggest that the contribution of PLA to range expansion may better explain plant invasion success than the level of PLA itself.     

Accelerated evolution of the electron transport chain in anthropoid primates

Mitochondria are both the power plant of the cell and a central integrator of signals that govern the lifespan, replication and death of the cell. Perhaps as a consequence, genes that encode components of the mitochondrial electron transport chain (ETC) are generally conserved. Therefore, it is surprising that many of these genes in anthropoid primates (New World monkeys, Old World monkeys and apes, including humans) have been major targets of darwinian positive selection. Sequence comparisons have provided evidence that marked increases of non-synonymous substitution rates occurred in anthropoid ETC genes that encode subunits of Complex III and IV, and the electron carrier molecule cytochrome c (CYC). Two important questions are: (i) how has evolution altered ETC function? and; (ii) how might functional changes in the ETC be linked to evolution of an expanded neocortical brain?     

Island biogeography extends to small-scale habitats: low competitor density and richness on islands may drive trait variation in nonnative plants

Previous island biogeography studies have quantified species richness on the scale of entire islands rather than smaller scales relevant to plant-to-plant competitive interactions. Further, they have not accounted for density compensation. Using mainland and island sites along the New England coast, we asked two questions. First, are both richness and density lower in small-scale habitats within islands than in similar mainland habitats? Second, do differences in competitor richness and density drive post-establishment trait variation in nonnative plant species? We used field surveys and individual-based rarefaction to estimate richness and density in 100-m² plots and demonstrated that island sites have significantly fewer species and individuals per unit area than mainland sites. We then conducted a field study in which we removed competing neighbors from nonnative plant individuals and found that when competitors were removed, individuals in low-competition environments demonstrated a lesser increase in vegetative growth but a greater increase in reproductive effort and herbivore tolerance relative to mainland individuals whose neighbors were also removed. We found that the central concept of island biogeography, i.e., that islands host fewer species than comparable mainland habitats, can be extended to smaller-scale habitats and that this difference in competitive pressure between mainland and island habitats can act as a driver of trait variation in nonnative plants.     

Oscillation,Conduction Delays,and Learning Cooperate to Establish Neural Competition in Recurrent Networks

Specific memory might be stored in a subnetwork consisting of a small population of neurons. To select neurons involved in memory formation, neural competition might be essential. In this paper, we show that excitable neurons are competitive and organize into two assemblies in a recurrent network with spike timing-dependent synaptic plasticity (STDP) and axonal conduction delays. Neural competition is established by the cooperation of spontaneously induced neural oscillation, axonal conduction delays, and STDP. We also suggest that the competition mechanism in this paper is one of the basic functions required to organize memory-storing subnetworks into fine-scale cortical networks.