What makes a model organism?

Telling Ecopoetic Stories: Wax Worms, Care, and the Cultivation of Other Sensibilities

Recently, a beekeeper discovered the metabolic wizardry of wax worms, their ability to decompose polyethylene. While this organism has usually been perceived as a model organism in science or a pest to beekeepers, it acquired a new mode of being as potentially probiotic, inviting us to dream of a future without plastic waste. In this paper, I explore how wax worms are entangled with material practices of care and narratives that give meaning to these practices. These stories, however, are marked by manipulation, exploitation, and extermination, and call for a questioning of our modes of caring. Consequently, I offer a counter-narrative that questions our anthropocentric practices of caring and the stories we attach to them. Borrowing Puig de la Bellacasa's notion of ecopoetics, I tell another story based on my participation in the making of an art installation hosting wax worms. The installation creates an opening of a world of curiosity and cultivates a sensibility for wax worms expanding their modes of being and our capabilities of appreciation. In the end, I argue that by mattering and storying differently, we have the opportunity to challenge anthropocentric interests and make a different world of caring and co-existence possible.

Daily activity profiles over the lifespan of female medflies as biomarkers of aging and longevity

The relationship between the early-age activity of Mediterranean fruit flies (medflies) or other fruit flies and their lifespan has not been much studied, in contrast to the connections between lifespan and diet, sexual signaling, and reproduction. The objective of this study is to assess intra-day and day-to-day activity profiles of female Mediterranean fruit flies and their role as biomarker of longevity as well as to explore the relationships between these activity profiles, diet, and age-at-death throughout the lifespan. We use advanced statistical methods from functional data analysis (FDA). Three distinct patterns of activity variations in early-age activity profiles can be distinguished. A low-caloric diet is associated with a delayed activity peak, while a high-caloric diet is linked with an earlier activity peak. We find that age-at-death of individual medflies is connected to their activity profiles in early life. An increased risk of mortality is associated with increased activity in early age, as well as with a higher contrast between daytime and nighttime activity. Conversely, medflies are more likely to have a longer lifespan when they are fed a medium-caloric diet and when their daily activity is more evenly distributed across the early-age span and between daytime and nighttime. The before-death activity profile of medflies displays two characteristic before-death patterns, where one pattern is characterized by slowly declining daily activity and the other by a sudden decline in activity that is followed by death.

Female behavior drives the formation of distinct social structures in C57BL/6J versus wild-derived outbred mice in field enclosures

BACKGROUND

Social behavior and social organization have major influences on individual health and fitness. Yet, biomedical research focuses on studying a few genotypes under impoverished social conditions. Understanding how lab conditions have modified social organizations of model organisms, such as lab mice, relative to natural populations is a missing link between socioecology and biomedical science.

RESULTS

Using a common garden design, we describe the formation of social structure in the well-studied laboratory mouse strain, C57BL/6J, in replicated mixed-sex populations over 10-day trials compared to control trials with wild-derived outbred house mice in outdoor field enclosures. We focus on three key features of mouse social systems: (i) territory establishment in males, (ii) female social relationships, and (iii) the social networks formed by the populations. Male territorial behaviors were similar but muted in C57 compared to wild-derived mice. Female C57 sharply differed from wild-derived females, showing little social bias toward cage mates and exploring substantially more of the enclosures compared to all other groups. Female behavior consistently generated denser social networks in C57 than in wild-derived mice.

CONCLUSIONS

C57 and wild-derived mice individually vary in their social and spatial behaviors which scale to shape overall social organization. The repeatable societies formed under field conditions highlights opportunities to experimentally study the interplay between society and individual biology using model organisms.

Immunosuppressive effect of Plantago major on the innate immunity of Galleria mellonella

Greater plantain (Plantago major), a medicinal plant species, is used in folk medicine for the treatment of various diseases in many countries of the world. Different studies have shown that the bioactive components contained in the plant have a dual effect. It was also reported that in vivo and in vitro studies showed different results. The aim of the study was to determine the effects of P. major extract on the hemocyte-mediated and humoral immune responses of the invertebrate model organism Galleria mellonella, which is widely used in immune studies. In the evaluation of these effects, total hemocyte count, encapsulation, melanization, phenoloxidase, superoxide dismutase, catalase, malondialdehyde and total protein parameters were evaluated. The results of the study showed that the total hemocyte count did not change, that the encapsulation responses decreased, that the melanization responses and phenoloxidase activity increased and that the superoxide dismutase activity decreased. As a result, it was determined that high doses of P. major had negative effects on cell-mediated immunity and antioxidant defence and positive effects on melanization. High doses and continuous use of P. major may have negative effects on living things.

Modelling the Tumour Microenvironment, but What Exactly Do We Mean by "Model"?

The Oxford English Dictionary includes 17 definitions for the word "model" as a noun and another 11 as a verb. Therefore, context is necessary to understand the meaning of the word model. For instance, "model railways" refer to replicas of railways and trains at a smaller scale and a "model student" refers to an exemplary individual. In some cases, a specific context, like cancer research, may not be sufficient to provide one specific meaning for model. Even if the context is narrowed, specifically, to research related to the tumour microenvironment, "model" can be understood in a wide variety of ways, from an animal model to a mathematical expression. This paper presents a review of different "models" of the tumour microenvironment, as grouped by different definitions of the word into four categories: model organisms, in vitro models, mathematical models and computational models. Then, the frequencies of different meanings of the word "model" related to the tumour microenvironment are measured from numbers of entries in the MEDLINE database of the United States National Library of Medicine at the National Institutes of Health. The frequencies of the main components of the microenvironment and the organ-related cancers modelled are also assessed quantitatively with specific keywords. Whilst animal models, particularly xenografts and mouse models, are the most commonly used "models", the number of these entries has been slowly decreasing. Mathematical models, as well as prognostic and risk models, follow in frequency, and these have been growing in use.

How molecular techniques are developed from natural systems

A striking characteristic of the molecular techniques of genetics is that they are derived from natural occurring systems. RNA interference, for example, utilizes a mechanism that evolved in eukaryotes to destroy foreign nucleic acid. Other case studies I highlight are restriction enzymes, DNA sequencing, polymerase chain reaction, gene targeting, fluorescent proteins (such as, green fluorescent protein), induced pluripotent stem cells, and clustered regularly interspaced short palindromic repeats-CRISPR associated 9. The natural systems' strategy for technique development means that biologists utilize the activity of a mechanism's effector (protein or RNA) and exploit biological specificity (protein or nucleic acid can cause precise reactions). I also argue that the developmental trajectory of novel molecular techniques, such as RNA interference, has 4 characteristic phases. The first phase is discovery of a biological phenomenon. The second phase is identification of the biological mechanism's trigger(s): the effector and biological specificity. The third phase is the application of the trigger(s) as a technique. The final phase is the maturation and refinement of the technique. Developing new molecular techniques from nature is crucial for future genetic research.

The Inverse Krogh Principle: All Organisms Are Worthy of Study

AbstractKrogh's principle states, "For such a large number of problems there will be some animal of choice, or a few such animals, on which it can be most conveniently studied." The downside of picking a question first and then finding an ideal organism on which to study it is that it will inevitably leave many organisms neglected. Here, we promote the inverse Krogh principle: all organisms are worthy of study. The inverse Krogh principle and the Krogh principle are not opposites. Rather, the inverse Krogh principle emphasizes a different starting point for research: start with a biological unit, such as an organism, clade, or specific organism trait, then seek or create tractable research questions. Even the hardest-to-study species have research questions that can be asked of them: Where does it fall within the tree of life? What resources does it need to survive and reproduce? How does it differ from close relatives? Does it have unique adaptations? The Krogh and inverse Krogh approaches are complementary, and many research programs naturally include both. Other considerations for picking a study species include extreme species, species informative for phylogenetic analyses, and the creation of models when a suitable species does not exist. The inverse Krogh principle also has pitfalls. A scientist that picks the organism first might choose a research question not really suited to the organism, and funding agencies rarely fund organism-centered grant proposals. The inverse Krogh principle does not call for all organisms to receive the same amount of research attention. As knowledge continues to accumulate, some organisms-models-will inevitably have more known about them than others. Rather, it urges a broader search across organismal diversity to find sources of inspiration for research questions and the motivation needed to pursue them.

Assessment of The Effect of Thymbra capitata Ethanolic Extract on Galleria mellonella Hemolymph Antioxidant Enzymes

Conehead thyme (Thymbra capitata) is widely distributed in the countries of the Mediterranean region and used due to its medical properties. The antibacterial, antifungal, and strong antioxidant properties of T. capitata are known. The model organism Galleria mellonella is mostly preferred for immunological studies and for the study of human pathogens. The aim of the study was to determine the effect of the ethanolic extract of T. capitata on the antioxidant defense of the hemolymph in G. mellonella larva. Solutions prepared with Phosphate-Buffered Saline (PBS) from the dry matter obtained from ethanolic extract at doses between 2 mg mL-1 and 20 mg mL-1 were injected into G. mellonella larvae. According to our findings, T. capitata extract had no effect on malondialdehyde (MDA) levels. However, it was determined that all doses between 10 to 20 mg mL-1 significantly reduced superoxide dismutase (SOD) and catalase (CAT) activities compared to the control groups. According to the results of our study, high doses of T. capitata extract had negative effects on G. mellonella antioxidant defense.

Harnessing the Power of Model Organisms To Unravel Microbial Functions in the Coral Holobiont

Stony corals build the framework of coral reefs, ecosystems of immense ecological and economic importance. The existence of these ecosystems is threatened by climate change and other anthropogenic stressors that manifest in microbial dysbiosis such as coral bleaching and disease, often leading to coral mortality. Despite a significant amount of research, the mechanisms ultimately underlying these destructive phenomena, and what could prevent or mitigate them, remain to be resolved. This is mostly due to practical challenges in experimentation on corals and the highly complex nature of the coral holobiont that also includes bacteria, archaea, protists, and viruses. While the overall importance of these partners is well recognized, their specific contributions to holobiont functioning and their interspecific dynamics remain largely unexplored. Here, we review the potential of adopting model organisms as more tractable systems to address these knowledge gaps. We draw on parallels from the broader biological and biomedical fields to guide the establishment, implementation, and integration of new and emerging model organisms with the aim of addressing the specific needs of coral research. We evaluate the cnidarian models Hydra, Aiptasia, Cassiopea, and Astrangia poculata; review the fast-evolving field of coral tissue and cell cultures; and propose a framework for the establishment of "true" tropical reef-building coral models. Based on this assessment, we also suggest future research to address key aspects limiting our ability to understand and hence improve the response of reef-building corals to future ocean conditions.

Electronic recording of lifetime locomotory activity patterns of adult medflies

Age-specific and diurnal patterns of locomotory activity, can be considered as biomarkers of aging in model organisms and vary across the lifetime of individuals. Τhe Mediterranean fruit fly (medfly), Ceratitis capitata, is a commonly used model-species in studies regarding demography and aging. In the present study, we introduce a modification of the automated locomotory activity electronic device LAM25system (Locomotory Activity Monitor)-Trikinetics, commonly used in short time studies, to record the daily locomotory activity patterns of adult medflies throughout the life. Additionally, fecundity rates and survival of adult medflies were recorded. Male and female medflies were kept in the system tubes and had access to an agar-based gel diet, which provided water and nutrients. The locomotory activity was recorded at every minute by three monitors in the electronic device. The locomotory activity of females was higher than that of males across the different ages. For both sexes locomotory rates were high during the first 20 days of the adult life and decreased in older ages. The activity of males was high in the morning and late afternoon hours, while that of females was constantly high throughout the photophase. Negligible locomotory activity was recorded for both sexes during the nighttime. Males outlived females. Fecundity of females was higher in younger ages. Our results support the adoption of LAM25system in studies addressing aging of insects using medfly as a model organism.

Development of an amphibian sperm biobanking protocol for genetic management and population sustainability

Sperm cryopreservation is a vital tool in amphibian assisted reproductive technologies that aids in genetic and population management, specifically for at-risk species. Significant advancements have been made in the cryopreservation of amphibian sperm, yet there is little information on how the cryopreservation process influences fertilization and embryonic development. In this study, we tested several cryoprotective agents (CPAs) and freezing rates on sperm recovery, fertilization potential and embryo development using Fowler's toads (Anaxyrus fowleri) as a model amphibian species for application to at-risk anurans. Three cryoprotectant treatments were tested, which included 10% trehalose + 0.25% bovine serum albumin with (1) 5% N,N-dimethylformamide (DMFA); (2) 10% DMFA; or (3) 10% dimethyl sulfoxide (DMSO). Additionally, sperm in each cryoprotectant was frozen at two different rates, -32 to -45°C/min and -20 to -29°C/min. Post-thaw sperm analysis included motility, morphology, viability, fertilization success and embryo development. Results show that 10% DMFA produced significantly higher (P = 0.005) post-thaw sperm motility than 5% DMFA and was similar to 10% DMSO. Furthermore, sperm frozen at -32 to -45°C/min had significantly higher post-thaw motility (P < 0.001) compared to sperm frozen at -20 to -29°C/min. We also found that embryos fertilized with sperm frozen with 5% DMFA resulted in significantly higher (P = 0.02) cleavage than 10% DMSO, yet there was no other effect of CPA on fertilization or embryo development. Furthermore, embryos fertilized with sperm frozen at -32 to -45°C/min resulted in significantly higher cleavage (P = 0.001), neurulation (P = 0.001) and hatching (P = 0.002) numbers than sperm frozen at a rate of -20 to -29°C/min. Overall, eggs fertilized with frozen-thawed sperm produced 1327 tadpoles. These results provide insight towards a biobanking strategy that can be applied to imperilled species to preserve genetic lineages and bolster offspring genetic diversity for reintroduction.

Transcriptional repression of TaNOX10 by TaWRKY19 compromises ROS generation and enhances wheat susceptibility to stripe rust

Reactive oxygen species (ROS) are vital for plant immunity and regulation of their production is crucial for plant health. While the mechanisms that elicit ROS production have been relatively well studied, those that repress ROS generation are less well understood. Here, via screening Brachypodium distachyon RNA interference mutants, we identified BdWRKY19 as a negative regulator of ROS generation whose knockdown confers elevated resistance to the rust fungus Puccinia brachypodii. The three wheat paralogous genes TaWRKY19 are induced during infection by virulent P. striiformis f. sp. tritici (Pst) and have partially redundant roles in resistance. The stable overexpression of TaWRKY19 in wheat increased susceptibility to an avirulent Pst race, while mutations in all three TaWRKY19 copies conferred strong resistance to Pst by enhancing host plant ROS accumulation. We show that TaWRKY19 is a transcriptional repressor that binds to a W-box element in the promoter of TaNOX10, which encodes an NADPH oxidase and is required for ROS generation and host resistance to Pst. Collectively, our findings reveal that TaWRKY19 compromises wheat resistance to the fungal pathogen and suggest TaWRKY19 as a potential target to improve wheat resistance to the commercially important wheat stripe rust fungus.

Belgica antarctica (Diptera: Chironomidae): A natural model organism for extreme environments

Belgica antarctica (Diptera: Chironomidae), a brachypterous midge endemic to the maritime Antarctic, was first described in 1900. Over more than a century of study, a vast amount of information has been compiled on the species (3 750 000 Google search results as of January 10, 2021), encompassing its ecology and biology, life cycle and reproduction, polytene chromosomes, physiology, biochemistry and, increasingly, omics. In 2014, B. antarctica's genome was sequenced, further boosting research. Certain developmental stages can be cultured successfully in the laboratory. Taken together, this wealth of information allows the species to be viewed as a natural model organism for studies of adaptation and function in extreme environments.

Adult insect personality in the wild-Calopteryx splendens as a model for field studies

Animal personality has received increasing interest and acknowledgment within ecological research over the past two decades. However, some areas are still poorly studied and need to be developed. For instance, field studies focused on invertebrates are currently highly underrepresented in the literature. More studies including a wider variety of traits measured and species tested are needed to improve our understanding of trait-correlation patterns and generalities. We studied nine behavioral traits, in the damselfly Calopteryx splendens, from an array of three experiments: (i) courtship, (ii) aggressiveness, and (iii) boldness, and calculated their repeatability. The behaviors were measured twice in two different contexts: (i) undisturbed territory and (ii) partially deteriorated territory. Traits related to courtship and boldness were all repeatable across the two contexts. Among aggressive behaviors, only one trait (number of hits) was repeatable. This work demonstrates, for the first time, the presence of within-population personality differences in an adult damselfly in the wild. We further propose C. splendens as a promising model species for testing personality in the wild under highly controlled environmental conditions.

Microfluidic chips: recent advances, critical strategies in design, applications and future perspectives

Microfluidic chip technology is an emerging tool in the field of biomedical application. Microfluidic chip includes a set of groves or microchannels that are engraved on different materials (glass, silicon, or polymers such as polydimethylsiloxane or PDMS, polymethylmethacrylate or PMMA). The microchannels forming the microfluidic chip are interconnected with each other for desired results. This organization of microchannels trapped into the microfluidic chip is associated with the outside by inputs and outputs penetrating through the chip, as an interface between the macro- and miniature world. With the help of a pump and a chip, microfluidic chip helps to determine the behavioral change of the microfluids. Inside the chip, there are microfluidic channels that permit the processing of the fluid, for example, blending and physicochemical responses. Microfluidic chip has numerous points of interest including lesser time and reagent utilization and alongside this, it can execute numerous activities simultaneously. The miniatured size of the chip fastens the reaction as the surface area increases. It is utilized in different biomedical applications such as food safety sensing, peptide analysis, tissue engineering, medical diagnosis, DNA purification, PCR activity, pregnancy, and glucose estimation. In the present study, the design of various microfluidic chips has been discussed along with their biomedical applications.

Scientific inertia in animal-based research in biomedicine

Despite aspirations to substitute animal experimentation with alternative methods and recent progress in the area of non-animal approaches, such as organoïds and organ(s)-on-a-chip technologies, there is no extensive replacement of animal-based research in biomedicine. In this paper, I will analyse this state of affairs with reference to key institutional and socio-epistemic barriers for the development and use of non-animal approaches in the context of biomedical research in Europe. I will argue that there exist several factors that inhibit change in this context. In particular, there is what I call "scientific inertia", i.e. a certain degree of conservatism in scientific practice regarding the development and use of non-animal approaches to replace animal experimentation. This type of inertia is facilitated by socio-epistemic characteristics of animal-based research in the life sciences and is a key factor in understanding the status quo in biomedical research. The underlying reasons for scientific inertia have not received sufficient attention in the literature to date because the phenomenon transcends traditional disciplinary boundaries in the study of animal experimentation. This paper addresses this issue and seeks to contribute to a better understanding of scientific inertia by using a methodology that looks at the interplay of institutional, epistemic, and regulatory aspects of animal-based research.

A Call for a Better Understanding of Aquatic Chytrid Biology

The phylum Chytridiomycota (the "chytrids") is an early-diverging, mostly unicellular, lineage of fungi that consists of significant aquatic saprotrophs, parasites, and pathogens, and is of evolutionary interest because its members retain biological traits considered ancestral in the fungal kingdom. While the existence of aquatic chytrids has long been known, their fundamental biology has received relatively little attention. We are beginning to establish a detailed understanding of aquatic chytrid diversity and insights into their ecological functions and prominence. However, the underpinning biology governing their aquatic ecological activities and associated core processes remain largely understudied and therefore unresolved. Many biological questions are outstanding for aquatic chytrids. What are the mechanisms that control their development and life cycle? Which core processes underpin their aquatic influence? What can their biology tell us about the evolution of fungi and the wider eukaryotic tree of life? We propose that the field of aquatic chytrid ecology could be further advanced through the improved understanding of chytrid biology, including the development of model aquatic chytrids and targeted studies using culture-independent approaches.

Lagomorpha as a Model Morphological System

Due to their global distribution, invasive history, and unique characteristics, European rabbits are recognizable almost anywhere on our planet. Although they are members of a much larger group of living and extinct mammals [Mammalia, Lagomorpha (rabbits, hares, and pikas)], the group is often characterized by several well-known genera (e.g., Oryctolagus, Sylvilagus, Lepus, and Ochotona). This representation does not capture the extraordinary diversity of behavior and form found throughout the order. Model organisms are commonly used as exemplars for biological research, but there are a limited number of model clades or lineages that have been used to study evolutionary morphology in a more explicitly comparative way. We present this review paper to show that lagomorphs are a strong system in which to study macro- and micro-scale patterns of morphological change within a clade that offers underappreciated levels of diversity. To this end, we offer a summary of the status of relevant aspects of lagomorph biology.

Model Systems in Ecology, Evolution, and Behavior: A Call for Diversity in Our Model Systems and Discipline

AbstractEcologists and evolutionary biologists are fascinated by life's variation but also seek to understand phenomena and mechanisms that apply broadly across taxa. Model systems can help us extract generalities from amid all the wondrous diversity, but only if we choose and develop them carefully, use them wisely, and have a range of model systems from which to choose. In this introduction to the Special Feature on Model Systems in Ecology, Evolution, and Behavior (EEB), we begin by grappling with the question, What is a model system? We then explore where our model systems come from, in terms of the skills and other attributes required to develop them and the historical biases that influence traditional model systems in EEB. We emphasize the importance of communities of scientists in the success of model systems-narrow scientific communities can restrict the model organisms themselves. We also consider how our discipline was built around one type of "model scientist"-a history still reflected in the field. This lack of diversity in EEB is unjust and also narrows the field's perspective, including by restricting the questions asked and talents used to answer them. Increasing diversity, equity, and inclusion will require acting at many levels, including structural changes. Diversity in EEB, in both model systems and the scientists who use them, strengthens our discipline.

The Use and Underuse of Model Systems in Infectious Disease Ecology and Evolutionary Biology

AbstractEver since biologists began studying the ecology and evolution of infectious diseases (EEID), laboratory-based model systems have been important for developing and testing theory. Yet what EEID researchers mean by the term "model systems" and what they want from them is unclear. This uncertainty hinders our ability to maximally exploit these systems, identify knowledge gaps, and establish effective new model systems. Here, we borrow a definition of model systems from the biomolecular sciences to assess how EEID researchers are (and are not) using 10 key model systems. According to this definition, model systems in EEID are not being used to their fullest and, in fact, cannot even be considered model systems. Research using these systems consistently addresses only two of the three fundamental processes that underlie disease dynamics-transmission and disease, but not recovery. Furthermore, studies tend to focus on only a few scales of biological organization that matter for disease ecology and evolution. Moreover, the field lacks an infrastructure to perform comparative analyses. We aim to begin a discussion of what we want from model systems, which would further progress toward a thorough, holistic understanding of EEID.

Defining comparative physiology: results from an online survey and systematic review

August Krogh's 1929 principle is referenced as the cornerstone of comparative physiology (CP). However, there are diverse views as to what type of research falls under the CP approach. This study had three aims: 1) determine how CP is defined through an online survey (OS) of physiologists and a systematic review (SR), 2) put forth an updated definition of CP by summarizing OS and SR results, and 3) outline the numerous CP research approaches. Professional physiology societies (n = 54) were invited to share the OS with their members, and a SR was conducted, which yielded 197 and 70 definitions, respectively. The three most common words in descending order in the OS definitions were "different," "animals," and "species" and in the SR definitions, "animals," "species," and "organisms." The three most prevalent themes from the OS and SR definitions were comparing/differences/diversity across species (78% and 51%, respectively), response to the environment/ecology (28% and 43%, respectively), and included evolution or adaptation (24% and 60%, respectively). Ten research approaches were identified, which include broad comparison (i.e., many species generalization), specific comparison (e.g., 2 species; for traits that are different, exaggerated, extreme, missing, or not induced), or comparison while considering evolution (i.e., evolutionary physiology), ecology (i.e., ecophysiology), or human physiology/medicine. Only 5% and 33% of OS and SR definitions described or mentioned Krogh's principle. In conclusion, CP can best be defined as a compilation of research approaches that utilize different types of comparisons to elucidate physiological mechanisms and not simply comparing physiologies as the name implies.

WITHDRAWN: Utilizing comparative models in biomedical research

The Publisher regrets that this article is an accidental duplication of an article that has already been published in Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, Volume 255, 2021, 110593, https://doi.org/10.1016/j.cbpb.2021.110593. The duplicate article has therefore been withdrawn. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.

Utilizing comparative models in biomedical research

This review serves as an introduction to a Special Issue of Comparative Biochemistry and Physiology, focused on using non-human models to study biomedical physiology. The concept of a model differs across disciplines. For example, several models are used primarily to gain an understanding of specific human pathologies and disease states, whereas other models may be focused on gaining insight into developmental or evolutionary mechanisms. It is often the case that animals initially used to gain knowledge of some unique biochemical or physiological process finds foothold in the biomedical community and becomes an established model. The choice of a particular model for biomedical research is an ongoing process and model validation must keep pace with existing and emerging technologies. While the importance of non-mammalian models, such as Caenorhabditis elegans, Drosophila melanogaster, Danio rerio and Xenopus laevis, is well known, we also seek to bring attention to emerging alternative models of both invertebrates and vertebrates, which are less established but of interest to the comparative biochemistry and physiology community.

The molecular vista: current perspectives on molecules and life in the twentieth century

This essay considers how scholarly approaches to the development of molecular biology have too often narrowed the historical aperture to genes, overlooking the ways in which other objects and processes contributed to the molecularization of life. From structural and dynamic studies of biomolecules to cellular membranes and organelles to metabolism and nutrition, new work by historians, philosophers, and STS scholars of the life sciences has revitalized older issues, such as the relationship of life to matter, or of physicochemical inquiries to biology. This scholarship points to a novel molecular vista that opens up a pluralist view of molecularizations in the twentieth century and considers their relevance to current science.

Factors influencing taxonomic unevenness in scientific research: a mixed-methods case study of non-human primate genomic sequence data generation

Scholars have noted major disparities in the extent of scientific research conducted among taxonomic groups. Such trends may cascade if future scientists gravitate towards study species with more data and resources already available. As new technologies emerge, do research studies employing these technologies continue these disparities? Here, using non-human primates as a case study, we identified disparities in massively parallel genomic sequencing data and conducted interviews with scientists who produced these data to learn their motivations when selecting study species. We tested whether variables including publication history and conservation status were significantly correlated with publicly available sequence data in the NCBI Sequence Read Archive (SRA). Of the 179.6 terabases (Tb) of sequence data in SRA for 519 non-human primate species, 135 Tb (approx. 75%) were from only five species: rhesus macaques, olive baboons, green monkeys, chimpanzees and crab-eating macaques. The strongest predictors of the amount of genomic data were the total number of non-medical publications (linear regression; r ² = 0.37; p = 6.15 × 10^-12) and number of medical publications (r ² = 0.27; p = 9.27 × 10^-9). In a generalized linear model, the number of non-medical publications (p = 0.00064) and closer phylogenetic distance to humans (p = 0.024) were the most predictive of the amount of genomic sequence data. We interviewed 33 authors of genomic data-producing publications and analysed their responses using grounded theory. Consistent with our quantitative results, authors mentioned their choice of species was motivated by sample accessibility, prior published work and relevance to human medicine. Our mixed-methods approach helped identify and contextualize some of the driving factors behind species-uneven patterns of scientific research, which can now be considered by funding agencies, scientific societies and research teams aiming to align their broader goals with future data generation efforts.

Genome size evolution: towards new model systems for old questions

Genome size (GS) variation is a fundamental biological characteristic; however, its evolutionary causes and consequences are the topic of ongoing debate. Whether GS is a neutral trait or one subject to selective pressures, and how strong these selective pressures are, may remain open questions. Fundamentally, the genomic sequences responsible for this variation directly impact the potential evolutionary outcomes and, equally, are the targets of different evolutionary pressures. For example, duplications and deletions of genic regions (large or small) can have immediate and drastic phenotypic effects, while an expansion or contraction of non-coding DNA is less likely to cause catastrophic phenotypic effects. However, in the long term, the accumulation or deletion of ncDNA is likely to have larger effects. Modern sequencing technologies are allowing for the dissection of these proximate causes, but a combination of these new technologies with more traditional evolutionary experiments and approaches could revolutionize this debate and potentially resolve many of these arguments. Here, I discuss an ambitious way forward for GS research, putting it in context of historical debates, theories and sometimes contradictory evidence, and highlighting the promise of combining new sequencing technologies and analytical developments with more traditional experimental evolution approaches.

Zebrafish Models in Neural and Behavioral Toxicology across the Life Stages

The industry is increasingly relying on fish for toxicity assessment. However, current guidelines for toxicity assessment focus on teratogenicity and mortality. From an ecotoxicological point of view, however, these endpoints may not reflect the “full picture” of possible deleterious effects that can nonetheless result in decreased fitness and/or inability to adapt to a changing environment, affecting whole populations. Therefore, assessing sublethal effects add relevant data covering different aspects of toxicity at different levels of analysis. The impacts of toxicants on neurobehavioral function have the potential to affect many different life-history traits, and are easier to assess in the laboratory than in the wild. We propose that carefully-controlled laboratory experiments on different behavioral domains—including anxiety, aggression, and exploration—can increase our understanding of the ecotoxicological impacts of contaminants, since these domains are related to traits such as defense, sociality, and reproduction, directly impacting life-history traits. The effects of selected contaminants on these tests are reviewed, focusing on larval and adult zebrafish, showing that these behavioral domains are highly sensitive to small concentrations of these substances. These strategies suggest a way forward on ecotoxicological research using fish.

Identifying adaptive alleles in the human genome: from selection mapping to functional validation

The suite of phenotypic diversity across geographically distributed human populations is the outcome of genetic drift, gene flow, and natural selection throughout human evolution. Human genetic variation underlying local biological adaptations to selective pressures is incompletely characterized. With the emergence of population genetics modeling of large-scale genomic data derived from diverse populations, scientists are able to map signatures of natural selection in the genome in a process known as selection mapping. Inferred selection signals further can be used to identify candidate functional alleles that underlie putative adaptive phenotypes. Phenotypic association, fine mapping, and functional experiments facilitate the identification of candidate adaptive alleles. Functional investigation of candidate adaptive variation using novel techniques in molecular biology is slowly beginning to unravel how selection signals translate to changes in biology that underlie the phenotypic spectrum of our species. In addition to informing evolutionary hypotheses of adaptation, the discovery and functional annotation of adaptive alleles also may be of clinical significance. While selection mapping efforts in non-European populations are growing, there remains a stark under-representation of diverse human populations in current public genomic databases, of both clinical and non-clinical cohorts. This lack of inclusion limits the study of human biological variation. Identifying and functionally validating candidate adaptive alleles in more global populations is necessary for understanding basic human biology and human disease.

Using automated reasoning to explore the metabolism of unconventional organisms: a first step to explore host-microbial interactions

Systems modelled in the context of molecular and cellular biology are difficult to represent with a single calibrated numerical model. Flux optimisation hypotheses have shown tremendous promise to accurately predict bacterial metabolism but they require a precise understanding of metabolic reactions occurring in the considered species. Unfortunately, this information may not be available for more complex organisms or non-cultured microorganisms such as those evidenced in microbiomes with metagenomic techniques. In both cases, flux optimisation techniques may not be applicable to elucidate systems functioning. In this context, we describe how automatic reasoning allows relevant features of an unconventional biological system to be identified despite a lack of data. A particular focus is put on the use of Answer Set Programming, a logic programming paradigm with combinatorial optimisation functionalities. We describe its usage to over-approximate metabolic responses of biological systems and solve gap-filling problems. In this review, we compare steady-states and Boolean abstractions of metabolic models and illustrate their complementarity via applications to the metabolic analysis of macro-algae. Ongoing applications of this formalism explore the emerging field of systems ecology, notably elucidating interactions between a consortium of microbes and a host organism. As the first step in this field, we will illustrate how the reduction in microbiotas according to expected metabolic phenotypes can be addressed with gap-filling problems.

Zygnematophyceae: from living algae collections to the establishment of future models

The class of conjugating green algae, Zygnematophyceae (Conjugatophyceae), is extremely rich in species and has attracted the interest of phycologists for a long time. It is now widely accepted that this class of charophyte algae holds a key position in the phylogenetic tree of streptophytes, where they represent the closest relatives to all land plants (embryophytes). It is increasingly evident that robust model plants that can be easily cultivated and genetically transformed are necessary to better understand the process of terrestrialization and the related molecular, cellular, and physiological adaptations. Living algae collections play an important role, not only for phylogenomic-based taxonomy but also for screening for suitable model organisms. For this review, we screened six major public algae collections for Zygnematophyceae strains and established a cumulative list comprising 738 different taxa (including species, subspecies, varieties, and forms). From the described biodiversity with 8883 registered taxa (AlgaeBase) the cultured Zygnematophyceae taxa worldwide cover only ~8.3%. We review the past research on this clade of algae and discuss it from the perspective of establishing a model organism. We present data on the life cycle of the genera Micrasterias and Spirogyra, representing the orders Desmidiales and Zygnematales, and outline the current status of genetic transformation of Zygnematophyceae algae and future research perspectives.

RefShannon: A genome-guided transcriptome assembler using sparse flow decomposition

High throughput sequencing of RNA (RNA-Seq) has become a staple in modern molecular biology, with applications not only in quantifying gene expression but also in isoform-level analysis of the RNA transcripts. To enable such an isoform-level analysis, a transcriptome assembly algorithm is utilized to stitch together the observed short reads into the corresponding transcripts. This task is complicated due to the complexity of alternative splicing - a mechanism by which the same gene may generate multiple distinct RNA transcripts. We develop a novel genome-guided transcriptome assembler, RefShannon, that exploits the varying abundances of the different transcripts, in enabling an accurate reconstruction of the transcripts. Our evaluation shows RefShannon is able to improve sensitivity effectively (up to 22%) at a given specificity in comparison with other state-of-the-art assemblers. RefShannon is written in Python and is available from Github (https://github.com/shunfumao/RefShannon).

Never the Two Shall Mix: Robust Indel Markers to Ensure the Fidelity of Two Pivotal and Closely-Related Accessions of Brachypodium distachyon

Brachypodium distachyon is an established model for monocotyledonous plants. Numerous markers intended for gene discovery and population genetics have been designed. However to date, very few indel markers with larger and easily scored length polymorphism differences, that distinguish between the two morphologically similar and highly utilized B. distachyon accessions, Bd21, the reference genome accession, and Bd21-3, the transformation-optimal accession, are publically available. In this study, 22 indel markers were designed and utilized to produce length polymorphism differences of 150 bp or more, for easy discrimination between Bd21 and Bd21-3. When tested on four other B. distachyon accessions, one case of multiallelism was observed. It was also shown that the markers could be used to determine homozygosity and heterozygosity at specific loci in a Bd21 x Bd3-1 F2 population. The work done in this study allows researchers to maintain the fidelity of Bd21 and Bd21-3 stocks for both transgenic and nontransgenic studies. It also provides markers that can be utilized in conjunction with others already available for further research on population genetics, gene discovery and gene characterization, all of which are necessary for the relevance of B. distachyon as a model species.

'Extreme' organisms and the problem of generalization: interpreting the Krogh principle

Many biologists appeal to the so-called Krogh principle when justifying their choice of experimental organisms. The principle states that "for a large number of problems there will be some animal of choice, or a few such animals, on which it can be most conveniently studied". Despite its popularity, the principle is often critiqued for implying unwarranted generalizations from optimal models. We argue that the Krogh principle should be interpreted in relation to the historical and scientific contexts in which it has been developed and used. We interpret the Krogh Principle as a heuristic, i.e., as a recommendation to approach biological problems through organisms where a specific trait or physiological mechanism is expected to be most distinctively displayed or most experimentally accessible. We designate these organisms "Krogh organisms". We clarify the differences between uses of model organisms and non-standard Krogh organisms. Among these is the use of Krogh organisms as "negative models" in biomedical research, where organisms are chosen for their dissimilarity to human physiology. Importantly, the representational scope of Krogh organisms and the generalizability of their characteristics are not fixed or assumed but explored through experimental studies. Research on Krogh organisms is steeped in the comparative method characteristic of zoology and comparative physiology, in which studies of biological variation produce insights into general physiological constraints. Accordingly, we conclude that the Krogh principle exemplifies the advantages of studying biological variation as a strategy to produce generalizable insights.

'Extreme' organisms and the problem of generalization: interpreting the Krogh principle

Many biologists appeal to the so-called Krogh principle when justifying their choice of experimental organisms. The principle states that "for a large number of problems there will be some animal of choice, or a few such animals, on which it can be most conveniently studied". Despite its popularity, the principle is often critiqued for implying unwarranted generalizations from optimal models. We argue that the Krogh principle should be interpreted in relation to the historical and scientific contexts in which it has been developed and used. We interpret the Krogh Principle as a heuristic, i.e., as a recommendation to approach biological problems through organisms where a specific trait or physiological mechanism is expected to be most distinctively displayed or most experimentally accessible. We designate these organisms "Krogh organisms". We clarify the differences between uses of model organisms and non-standard Krogh organisms. Among these is the use of Krogh organisms as "negative models" in biomedical research, where organisms are chosen for their dissimilarity to human physiology. Importantly, the representational scope of Krogh organisms and the generalizability of their characteristics are not fixed or assumed but explored through experimental studies. Research on Krogh organisms is steeped in the comparative method characteristic of zoology and comparative physiology, in which studies of biological variation produce insights into general physiological constraints. Accordingly, we conclude that the Krogh principle exemplifies the advantages of studying biological variation as a strategy to produce generalizable insights.

Quantitative Perspectives on Fifty Years of the Journal of the History of Biology

Journal of the History of Biology provides a fifty-year long record for examining the evolution of the history of biology as a scholarly discipline. In this paper, we present a new dataset and preliminary quantitative analysis of the thematic content of JHB from the perspectives of geography, organisms, and thematic fields. The geographic diversity of authors whose work appears in JHB has increased steadily since 1968, but the geographic coverage of the content of JHB articles remains strongly lopsided toward the United States, United Kingdom, and western Europe and has diversified much less dramatically over time. The taxonomic diversity of organisms discussed in JHB increased steadily between 1968 and the late 1990s but declined in later years, mirroring broader patterns of diversification previously reported in the biomedical research literature. Finally, we used a combination of topic modeling and nonlinear dimensionality reduction techniques to develop a model of multi-article fields within JHB. We found evidence for directional changes in the representation of fields on multiple scales. The diversity of JHB with regard to the representation of thematic fields has increased overall, with most of that diversification occurring in recent years. Drawing on the dataset generated in the course of this analysis, as well as web services in the emerging digital history and philosophy of science ecosystem, we have developed an interactive web platform for exploring the content of JHB, and we provide a brief overview of the platform in this article. As a whole, the data and analyses presented here provide a starting-place for further critical reflection on the evolution of the history of biology over the past half-century.

Corpos comensuráveis: produção de modelos animais nas ciências biomédicas

Resumo: A utilização de modelo animal, em especial camundongos e ratos, é uma prática consolidada nas pesquisas biomédicas, que visam, usualmente, caracterizar processos biológicos ou testar tratamentos, medicamentos em animais não humanos antes de verificar se os resultados se aplicam aos humanos. Tal uso de animais se assenta na proximidade genética entre humanos e roedores, portanto, na suposição de que os processos biológicos de humanos e animais são similares. Os corpos dos animais são tratados como substitutos ou representativos dos humanos, mas isso não significa dizer que são apenas representações cognitivas, eles são também encarnações de ações e práticas que constituem tipos de questões científicas e indicam que perguntas podem ser respondidas. O que este trabalho pretende interrogar são os modos práticos de produção de modelos animais. Como os animais se tornam portadores de doenças relevantes para os humanos? Como tornar seus corpos comensuráveis aos nossos?

Non-mammalian models in behavioral neuroscience: consequences for biological psychiatry

Current models in biological psychiatry focus on a handful of model species, and the majority of work relies on data generated in rodents. However, in the same sense that a comparative approach to neuroanatomy allows for the identification of patterns of brain organization, the inclusion of other species and an adoption of comparative viewpoints in behavioral neuroscience could also lead to increases in knowledge relevant to biological psychiatry. Specifically, this approach could help to identify conserved features of brain structure and behavior, as well as to understand how variation in gene expression or developmental trajectories relates to variation in brain and behavior pertinent to psychiatric disorders. To achieve this goal, the current focus on mammalian species must be expanded to include other species, including non-mammalian taxa. In this article, we review behavioral neuroscientific experiments in non-mammalian species, including traditional "model organisms" (zebrafish and Drosophila) as well as in other species which can be used as "reference." The application of these domains in biological psychiatry and their translational relevance is considered.

Publication trends in model organism research

In 1990, the National Institutes of Health (NIH) gave some organisms special status as designated model organisms. This article documents publication trends for these NIH-designated model organisms over the past 40 years. We find that being designated a model organism by the NIH does not guarantee an increasing publication trend. An analysis of model and nonmodel organisms included in GENETICS since 1960 does reveal a sharp decline in the number of publications using nonmodel organisms yet no decline in the overall species diversity. We suggest that organisms with successful publication records tend to share critical characteristics, such as being well developed as standardized, experimental systems and being used by well-organized communities with good networks of exchange and methods of communication.