What is in a model?

After reading contradictory claims of model status for some insect species, we feel a brief discussion of the topic may be useful. Here, we document a few examples where clarity on model status seems to be lacking, briefly review work on widely recognized models, and offer criteria for including any given species as a model organism.     

Terminology—A plea for consistency

Editorial

Terminology—A plea for consistency     

What do warming waters mean for fish physiology and fisheries?

Environmental signals act primarily on physiological systems, which then influence higher-level functions such as movement patterns and population dynamics. Increases in average temperature and temperature variability associated with global climate change are likely to have strong effects on fish physiology and thereby on populations and fisheries. Here we review the principal mechanisms that transduce temperature signals and the physiological responses to those signals in fish. Temperature has a direct, thermodynamic effect on biochemical reaction rates. Nonetheless, plastic responses to longer-term thermal signals mean that fishes can modulate their acute thermal responses to compensate at least partially for thermodynamic effects. Energetics are particularly relevant for growth and movement, and therefore for fisheries, and temperature can have pronounced effects on energy metabolism. All energy (ATP) production is ultimately linked to mitochondria, and temperature has pronounced effects on mitochondrial efficiency and maximal capacities. Mitochondria are dependent on oxygen as the ultimate electron acceptor so that cardiovascular function and oxygen delivery link environmental inputs with energy metabolism. Growth efficiency, that is the conversion of food into tissue, changes with temperature, and there are indications that warmer water leads to decreased conversion efficiencies. Moreover, movement and migration of fish relies on muscle function, which is partially dependent on ATP production but also on intracellular calcium cycling within the myocyte. Neuroendocrine processes link environmental signals to regulated responses at the level of different tissues, including muscle. These physiological processes within individuals can scale up to population responses to climate change. A mechanistic understanding of thermal responses is essential to predict the vulnerability of species and populations to climate change.     

What is a suitable management for Typha latifolia control in wet meadows?

Aim

Typha latifolia causes serious problems in wet meadows by overgrowing and suppressing other native plants. To determine suitable management for T. latifolia control, we addressed the following question: What are the effects of long-term cutting at different frequencies (once or twice per year and no management) and biomass removal on cover and other characteristics of T. latifolia, and on sward productivity and plant species composition?

Location

Malá Strana nature reserve, Jizerské hory Mountains, Czechia.

Methods

A long-term experiment arranged in a randomised block design with three blocks was established in 2005. Data were collected from five treatments: unmanaged control; cutting once a year in June without biomass removal and with biomass removal; cutting twice per year in June and August without biomass removal and with biomass removal. Percentage cover of T. latifolia and other vascular plant species was visually estimated and T. latifolia characteristics (tiller density, height, dry-matter biomass [DMB] yield and litter), sward height and DMB yield were measured during 2005–2018 at the end of June.

Results and Discussion

Regular cutting once or twice per year regardless of cut biomass removal led to reductions in tiller density, height, litter and DMB yield of T. latifolia. Biomass removal had only a slight tendency to affect T. latifolia characteristics. The higher frequency of cutting significantly decreased the mean T. latifolia cover, litter and DMB yield. Cutting once or twice per year regardless of biomass removal led to successive changes in plant species composition but had no effect on the species richness and evenness.

Conclusions

Cutting at least once per year without biomass removal seems to be sufficient to achieve a decrease in DMB yield and litter of T. latifolia plants, and thereby maintain the wet-meadow vegetation without loss of species richness and also preventing the overgrowth of shrubs and trees.     

The Hydra model - a model for what?

The introductory personal remarks refer to my motivations for choosing research projects, and for moving from physics to molecular biology and then to development, with Hydra as a model system. Historically, Trembley's discovery of Hydra regeneration in 1744 was the beginning of developmental biology as we understand it, with passionate debates about preformation versus de novo generation, mechanisms versus organisms. In fact, seemingly conflicting bottom-up and top-down concepts are both required in combination to understand development. In modern terms, this means analysing the molecules involved, as well as searching for physical principles underlying development within systems of molecules, cells and tissues. During the last decade, molecular biology has provided surprising and impressive evidence that the same types of molecules and molecular systems are involved in pattern formation in a wide range of organisms, including coelenterates like Hydra, and thus appear to have been "invented" early in evolution. Likewise, the features of certain systems, especially those of developmental regulation, are found in many different organisms. This includes the generation of spatial structures by the interplay of self-enhancing activation and "lateral" inhibitory effects of wider range, which is a main topic of my essay. Hydra regeneration is a particularly clear model for the formation of defined patterns within initially near-uniform tissues. In conclusion, this essay emphasizes the analysis of development in terms of physical laws, including the application of mathematics, and insists that Hydra was, and will continue to be, a rewarding model for understanding general features of embryogenesis and regeneration.     

Seals and fisheries: A case for predator control?

The impact of seals on fisheries has been a controversial matter. This article examines the degree to which a new Canadian Royal Commission Report has been able to judge between the opposing views of the problem. It also examines the implications of the Commission's results for the more general question of controlling predators for the benefit of prey species, or more accurately, the human harvesters of those species. Finally, it touches very briefly on the possible clash of views between the public at large and those who make their living from the sea.     

Fishery discards and bycatch: solutions for an ecosystem approach to fisheries management?

It has been widely acknowledged that fishery discard practices constitute a purposeless waste of valuable living resources, which plays an important role in the depletion of marine populations. Furthermore, discarding may have a number of adverse ecological impacts in marine ecosystems, provoking changes in the overall structure of trophic webs and habitats, which in turn could pose risks for the sustainability of current fisheries. The present review aims to describe the current state-of-the-art in discards research, with particular emphasis on the needs and challenges associated with the implementation of the Ecosystem Approach to Fisheries Management (EAFM) in European waters. We briefly review the international and European policy contexts of discarding, how discard data are collected and incorporated into stock assessments, selectivity in fishing and the main consequences of discarding for ecosystem dynamics. We then review implementation issues related to reducing discards under the EAFM and the associated scientific challenges, and conclude with some comments on lessons learned and future directions.     

Does the anterior cruciate have a modeling threshold? A case for the affirmative

Growing evidence supports a 1972 proposal that dynamic tension strains of a ligament above a threshold range, but below its ultimate strength, would make its cells synthesize more collagen to thicken and strengthen it. If so, when that strengthening reduced later strains to the bottom of that threshold range this "diametric modeling" would stop. A) Such a mechanism must create a "strength-safety factor" that would minimize or prevent voluntary activities from rupturing healthy ligaments, so chiefly injuries would rupture them. B) Such a mechanism should also make the usual largest loads on a healthy anterior cruciate ligament (ACL) determine its strength, and would make smaller loads mixed with large ones have little effect on its strength. C) In principle, when an ACL's strains exceeded that threshold range, diametric modeling would turn on, strengthen it, and reduce subsequent strains from the same loads. When its strains remained smaller, this mechanically-controlled modeling would turn off. Normal ACLs do have a strength-safety factor so they could have a diametric modeling threshold too, as we now know bone does. In healthy young adult humans available evidence suggests that threshold's value could lie in the region of 23 Newtons/mmC of the ACL's cross section area. If similar relationships applied to fascia, tendons and other ligaments (I suggest they do), they would form fundamental biomechanical properties of collagenous tissue organs.     

What drives adoption of a computerised,multifaceted quality improvement intervention for cardiovascular disease management in primary healthcare settings? A mixed methods analysis using normalisation process theory

Background

A computerised, multifaceted quality improvement (QI) intervention for cardiovascular disease (CVD) management in Australian primary healthcare was evaluated in a cluster randomised controlled trial. The intervention was associated with improved CVD risk factor screening but there was no improvement in prescribing rates of guideline-recommended medicines. The aim of this study was to conduct a process evaluation to identify and explain the underlying mechanisms by which the intervention did and did not have an impact.

Methods/design

Normalisation process theory (NPT) was used to understand factors that supported or constrained normalisation of the intervention into routine practice. A case study design was used in which six of the 30 participating intervention sites were purposively sampled to obtain a mix of size, governance, structure and performance. Multiple data sources were drawn on including trial outcome data, surveys of job satisfaction and team climate (68 staff) and in-depth interviews (19 staff). Data were primarily analysed within cases and compared with quantitative findings in other trial intervention and usual care sites.

Results

We found a complex interaction between implementation processes and several contextual factors affecting uptake of the intervention. There was no clear association between team climate, job satisfaction and intervention outcomes. There were four spheres of influence that appeared to enhance or detract from normalisation of the intervention: organisational mission and history (e.g. strategic investment to promote a QI culture enhanced cognitive participation), leadership (e.g. ability to energise or demotivate others influenced coherence), team environment (e.g. synergistic activities of team members with different skill sets influenced collective action) and technical integrity of the intervention (e.g. tools that slowed computer systems limited reflective action).

Discussion

Use of NPT helped explain how certain contextual factors influence the work that is done by individuals and teams when implementing a novel intervention. Although these factors do not necessarily distil into a recipe for successful uptake, they may assist system planners, intervention developers, and health professionals to better understand the trajectory that primary health care services may take when developing and engaging with QI interventions.

Trial registration

ACTRN 12611000478910. Registered 08 May 2011.

     

Are soil lichen communities structured by biotic interactions? A null model analysis

Question: Are soil lichen communities structured by biotic interactions? Location: Gypsum outcrops located next to Belmonte del Tajo, central Spain. Methods: We sampled a total of 68 (50 cm × 50 cm) plots in gypsum outcrops from central Spain. Each plot was divided into 100 (5 cm × 5 cm) sampling quadrats, and the presence of all lichen species in every quadrat was recorded (6800 quadrats in total). We used two realistic null models to generate random communities unstructured by biotic interactions, and used them to test the hypothesis that soil lichen species co‐occur less often than expected by chance. Results: We found fewer species combinations and less co‐occurrence than expected by chance. However, the latter result was dependent on the null model selected. The number of checkerboard pairs did not differ significantly from the null expectation. Conclusions: Overall, our results suggest that gypsiferous soil lichen communities are structured by competitive interactions. They are consistent with studies conducted with a wide variety of taxa, and fill a gap in our knowledge of the factors driving the small‐scale distribution of these important organisms.     

What is life? Prerequisites for a definition

Biologists view life as transient while theologians see it as eternal. An unbiased definition for life would respect both views until one or both were eliminated by evidence. This paper identifies pre-requisites for such a definition. First among these is that all assumptions be made explicit. Currently "life" is surrounded by implicit assumptions, e.g., that it is what organisms lose at death or that it is eternal, that its quality is inversely related to personal distress, that it originated some four billion years ago, and that animate matter can be distinguished from inanimate matter. None of these assumptions are supported by data. It is possible therefore that "life" is as meaningless as phlogiston. If life has meaning, i.e., if it is true, it must be as permanent as buoyancy, gravity, electricity, and the other truths of nature. Any definition for life that would permit such truth to be seen must be free of unwarranted assumptions. For the moment, at least, such a definition would need to be loosely structured and broadly focused. It would need to describe the long and convoluted process by which matter and energy form organisms which then evolve to form conscious organisms which then explore nature and eventually discover truth. Such a definition would include all the reactions and interactions of matter and energy and all the aspects of conscious discovery. It would suffer from superficiality, but, by being free from bias, provide a foundation for dialogue between biologists and theologians.     

Homing pigeons as a model for avian navigation?

The findings on the navigational mechanisms of homing pigeons and the available data on those of wild birds, in particular migrants, are compared. There are important parallels in the use of the magnetic field and the sun for directional orientation. Also the findings on the navigational ‘map’, its preferred use by experienced birds and the strategy of using route information to acquire the necessary knowledge to establish the ‘map’, obtained in pigeons studies, can probably be generalized to wild birds and migrants in their home region. It seems that birds share a common navigational system. Special development of migratory birds, however, is the innate migration program that enables young first‐time migrants to reach their still unknown wintering area.     

Cucumber: a model angiosperm for mitochondrial transformation?

Plants possess three major genomes, carried in the chloroplast, mitochondrion, and nucleus. The chloroplast genomes of higher plants tend to be of similar sizes and structure. In contrast both the nuclear and mitochondrial genomes show great size differences, even among closely related species. The largest plant mitochondrial genomes exist in the genus Cucumis at 1500 to 2300 kilobases, over 100 times the sizes of the yeast or human mitochondrial genomes. Biochemical and molecular analyses have established that the huge Cucumis mitochondrial genomes are due to extensive duplication of short repetitive DNA motifs. The organellar genomes of almost all organisms are maternally transmitted and few methods exist to manipulate these important genomes. Although chloroplast transformation has been achieved, no routine method exists to transform the mitochondrial genome of higher plants. A mitochondrial-transformation system for a higher plant would allow geneticists to use reverse genetics to study mitochondrial gene expression and to establish the efficacy of engineered mitochondrial genes for the genetic improvement of the mitochondrial genome. Cucumber possesses three unique attributes that make it a potential model system for mitochondrial transformation of a higher plant. Firstly, its mitochondria show paternal transmission. Secondly, microspores possess relatively few, huge mitochondria. Finally, there exists in cucumber unique mitochondrial mutations conditioning strongly mosaic (msc) phenotypes. The msc phenotypes appear after regeneration of plants from cell culture and sort with specific rearranged and deleted regions in the mitochondrial genome. These mitochondrial deletions may be a useful genetic tool to develop selectable markers for mitochondrial transformation of higher plants.     

Are microRNAs responsible for cardiac hypertrophy in fish and mammals? What we can learn in the activation process in a zebrafish ex vivo model

Recent studies have correlated dysregulated miRNA expression with diseased hearts. With the aim of developing an easily manipulated experimental model, phenylephrine (PE) was added to cultured zebrafish hearts to study the expression of miR1 and miR133a by qRT-PCR. Both miRs were downregulated, with greater downregulation leading to higher hypertrophy. The involvement of this miRs was confirmed by the in-vivo inoculation of complementary sequences (AmiR1 and AmiR133a). HSP70 (involved in transporting proteins and in anti-apoptosis processes) was increased in both treatments. Hyperplasia was observed in the epicardium based on WT1 expression (embryonic epicardial cell marker) in both the PE treatment and AmiR133a treatment. The treatment with AmiR1 showed only cardiomyocyte hypertrophy. This ex-vivo model revealed that miR1 and miR133a play a key role in activating early processes leading to myocardium hypertrophy and epicardium hyperplasia and confirmed the expected similarities with hypertrophic disease that occurs in humans.     

Mathematical modelling — a management tool for aquatic ecosystems?

Mathematical modelling may serve as a rational and powerful tool in the management of complex ecosystems. However, ecosystem models are drastic simplifications of the real world. As a rule they are based on a rather incomplete and scattered knowledge of the system in question. Furthermore, ecological systems and in particular marine systems are characterised by a high degree of complexity, spatial and functional heterogeneity, nonlinearity, complex behavioural features such as adptation and self-organisation, and a considerable stochastic element. Nevertheless, if management is to be based on predictions from mathematical models — and it has to be based on some kind of model in at least a broad sense — we need an estimate of prediction accuracy in terms of the management variables and constraints. One possible approach to model uncertainty is a probabilistic interpretation of model predictions, generated by use of Monte-Carlo techniques. Fuzzy data sets and ranges are used. The resulting model response allows the derivation of measures for model credibility. Probability distributions can be computed for certain system states under (un)certain input conditions, representing the effects of insufficient data and structural uncertainty on model-based predictions. Such analysis indicates that prediction uncertainty increases, not only with the uncertainty in the data, but also with increasing distance from the empirical conditions, and with time. Present ecoystem models can be a tool for qualitative discrimination between different management alternatives, rather than a credible means for detailed quantitative predictions of system response to a wide range of input conditions.