Experimental Organisms Research Articles

Adapting to change: insights from new organisms in cell and developmental biology.

We are living in an era of environmental change with undeniable parallels with past mass extinctions. To improve our understanding of planetary health and resilience, we must expand our research beyond traditional lab models. Forecasting the future of biological diversity relies on extrapolation of past trends, which necessitates the study of a wider range of biological systems. The 'Unconventional and Emerging Experimental Organisms for Cell and Developmental Biology' meeting, which took place in Dorking, UK, in September 2023, emphasized the importance of this broader approach. Discussions centered on evolutionary innovation, robustness and diversity, underscoring the need for broader taxon sampling and novel experimental models to address current and future challenges.

Pathway to independence: perspectives on the future.

In this Perspective, our 2024 Pathway to Independence Fellows provide their thoughts on the future of their field. Covering topics as diverse as plant development, tissue engineering and adaptation to climate change, and using a wide range of experimental organisms, these talented postdocs showcase some of the major open questions and key challenges across the spectrum of developmental biology research.

Bioactivity evaluations from stem bark extract fractions of Myrica esculenta Buch. ‐Ham.ex D. Don

AbstractThe chemical constituents of Myrica esculenta (a plant distributed across Nepal, India, China, and Pakistan) are known for their potent antioxidant properties and reported pharmacological effects. The study used methanol extract to assess antioxidant activity (DPPH assay), anthelmintic effects (standard; albendazole and experimental organism; Eisenia fetida), anti‐inflammatory properties (human red blood cell membrane stabilization), and cytotoxicity (brine shrimp lethality bioassay). The study revealed 39.06% yield with methanol and 2.01% with hexane. Phenolic and flavonoid content were measured at 96.43 mg GAE/g and 14.54 mg QE/g, respectively. Methanolic extract exhibited IC50 of 60.89 μg/mL and LC5o of 160.5298 μg/mL. It also demonstrated anti‐inflammatory activity, notably achieving a 37.8% membrane stabilizing action at 500 μg/mL. Anthelmintic potential was observed at different concentrations (50 mg/mL, 75 mg/mL, and 100 mg/mL), leading to paralysis and death of worms with corresponding times reported. Brine Shrimp Lethality Bioassay revealed concentration‐dependent effects. Methanolic extract of M. esculenta displayed robust antioxidant and anthelmintic activities. The extract was identified as bioactive, holding promise as a source for plant‐derived antitumor compounds. However, further investigation is essential to validate these findings.

MousebreedeR: A novel software to assist in the design of breeding schema for complex genotypes of experimental organisms

MousebreedeR: A novel software to assist in the design of breeding schema for complex genotypes of experimental organisms

Actin depolymerizing factor destrin governs cell migration in neural development during Xenopus embryogenesis

The actin-based cytoskeleton is considered a fundamental driving force for cell differentiation and development. Destrin (dstn), a member of the actin depolymerizing factor family, regulates actin dynamics by treadmilling actin filaments and increasing globular actin pools. However, the specific developmental roles of dstn have yet to be fully elucidated. Here, we investigated the physiological functions of dstn during early embryonic development using Xenopus laevis as an experimental model organism. dstn is expressed in anterior neural tissue and neural plate during Xenopus embryogenesis. Depleting dstn promoted morphants with short body axes and small heads. Moreover, dstn inhibition extended the neural plate region, impairing cell migration and distribution during neurulation. In addition to the neural plate, dstn knockdown perturbed neural crest cell migration. Our data suggest new insights for understanding the roles of actin dynamics in embryonic neural development, simultaneously presenting a new challenge for studying the complex networks governing cell migration involving actin dynamics.

The reference genome of Macropodus opercularis (the paradise fish)

Amongst fishes, zebrafish (Danio rerio) has gained popularity as a model system over most other species and while their value as a model is well documented, their usefulness is limited in certain fields of research such as behavior. By embracing other, less conventional experimental organisms, opportunities arise to gain broader insights into evolution and development, as well as studying behavioral aspects not available in current popular model systems. The anabantoid paradise fish (Macropodus opercularis), an “air-breather” species has a highly complex behavioral repertoire and has been the subject of many ethological investigations but lacks genomic resources. Here we report the reference genome assembly of M. opercularis using long-read sequences at 150-fold coverage. The final assembly consisted of 483,077,705 base pairs (~483 Mb) on 152 contigs. Within the assembled genome we identified and annotated 20,157 protein coding genes and assigned ~90% of them to orthogroups.

Dermal Dive: An Overview of Cutaneous Wounding Techniques in Zebrafish

Cutaneous wounds are common injuries that affect millions of people around the world. In vulnerable populations such as the elderly and those with diabetes, defects in wound healing can lead to the development of chronic open wounds. Although mammalian models are commonly used to study cutaneous wound healing, the challenges of invivo imaging in mammals have hampered detailed observation of cell coordination and cell signaling during wound healing. The zebrafish is becoming increasingly popular for studying cutaneous wound healing owing to its genetic accessibility, suitability for experimental manipulation, and the ability to perform live, invivo imaging with cellular or even subcellular resolution. In this paper, we review some of the techniques that have been developed for eliciting cutaneous wounds in the zebrafish, including an economical method we recently developed using a rotary tool that generates consistent and reproducible full-thickness wounds. Combined with the thousands of transgenic lines and experimental assays available in zebrafish, the ability to generate reproducible cutaneous wounds makes it possible to study key cellular and molecular events during wound healing using this powerful experimental model organism.

Transcriptional programs mediating neuronal toxicity and altered glial-neuronal signaling in a Drosophila knock-in tauopathy model.

Missense mutations in the gene encoding the microtubule-associated protein TAU (current and approved symbol is MAPT) cause autosomal dominant forms of frontotemporal dementia. Multiple models of frontotemporal dementia based on transgenic expression of human TAU in experimental model organisms, including Drosophila, have been described. These models replicate key features of the human disease but do not faithfully recreate the genetic context of the human disorder. Here we use CRISPR-Cas-mediated gene editing to model frontotemporal dementia caused by the TAU P301L mutation by creating the orthologous mutation, P251L, in the endogenous Drosophila tau gene. Flies heterozygous or homozygous for Tau P251L display age-dependent neurodegeneration, display metabolic defects, and accumulate DNA damage in affected neurons. To understand the molecular events promoting neuronal dysfunction and death in knock-in flies, we performed single-cell RNA sequencing on approximately 130,000 cells from brains of Tau P251L mutant and control flies. We found that expression of disease-associated mutant tau altered gene expression cell autonomously in all neuronal cell types identified. Gene expression was also altered in glial cells, suggestive of non-cell-autonomous regulation. Cell signaling pathways, including glial-neuronal signaling, were broadly dysregulated as were brain region and cell type-specific protein interaction networks and gene regulatory programs. In summary, we present here a genetic model of tauopathy that faithfully recapitulates the genetic context and phenotypic features of the human disease, and use the results of comprehensive single-cell sequencing analysis to outline pathways of neurotoxicity and highlight the potential role of non-cell-autonomous changes in glia.

A bioinformatics approach to elucidate conserved genes and pathways in C. elegans as an animal model for cardiovascular research

Cardiovascular disease (CVD) is a collective term for disorders of the heart and blood vessels. The molecular events and biochemical pathways associated with CVD are difficult to study in clinical settings on patients and in vitro conditions. Animal models play a pivotal and indispensable role in CVD research. Caenorhabditis elegans, a nematode species, has emerged as a prominent experimental organism widely utilized in various biomedical research fields. However, the specific number of CVD-related genes and pathways within the C. elegans genome remains undisclosed to date, limiting its in-depth utilization for investigations. In the present study, we conducted a comprehensive analysis of genes and pathways related to CVD within the genomes of humans and C. elegans through a systematic bioinformatic approach. A total of 1113 genes in C. elegans orthologous to the most significant CVD-related genes in humans were identified, and the GO terms and pathways were compared to study the pathways that are conserved between the two species. In order to infer the functions of CVD-related orthologous genes in C. elegans, a PPI network was constructed. Orthologous gene PPI network analysis results reveal the hubs and important KRs: pmk-1, daf-21, gpb-1, crh-1, enpl-1,eef-1G, acdh-8, hif-1, pmk-2, and aha-1 in C. elegans. Modules were identified for determining the role of the orthologous genes at various levels in the created network. We also identified 9 commonly enriched pathways between humans and C. elegans linked with CVDs that include autophagy (animal), the ErbB signaling pathway, the FoxO signaling pathway, the MAPK signaling pathway, ABC transporters, the biosynthesis of unsaturated fatty acids, fatty acid metabolism, glutathione metabolism, and metabolic pathways. This study provides the first systematic genomic approach to explore the CVD-associated genes and pathways that are present in C. elegans, supporting the use of C. elegans as a prominent animal model organism for cardiovascular diseases.

The complexities of ligand/receptor interactions: Exploring the role of molecular vibrations and quantum tunnelling.

Molecular vibrations and quantum tunneling may link ligand binding to the function of pharmacological receptors. The well-established lock-and-key model explains a ligand's binding and recognition by a receptor; however, a general mechanism by which receptors translate binding into activation, inactivation, or modulation remains elusive. The Vibration Theory of Olfaction was proposed in the 1930s to explain this subset of receptor-mediated phenomena by correlating odorant molecular vibrations to smell, but a mechanism was lacking. In the 1990s, inelastic electron tunneling was proposed as a plausible mechanism for translating molecular vibration to odorant physiology. More recently, studies of ligands' vibrational spectra and the use of deuterated ligand analogs have provided helpful information to study this admittedly controversial hypothesis in metabotropic receptors other than olfactory receptors. In the present work, based in part on published experiments from our laboratory using planarians as an experimental organism, I will present a rationale and possible experimental approach for extending this idea to ligand-gated ion channels.

Bioinspired stormwater control measure for the enhanced removal of truly dissolved polycyclic aromatic hydrocarbons and heavy metals from urban runoff

Stormwater harvesting (SWH) addresses the UN's Sustainable Development Goals (SDGs). Conventional stormwater control measures (SCMs) effectively remove particulate and colloidal contaminants from urban runoff; however, they fail to retain dissolved contaminants, particularly substances of concern like polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs), thereby hindering the SWH applicability. Here, inspired by protein folding in nature, we reported a novel biomimetic SCM for the efficient removal of dissolved PAHs and HMs from urban runoff. Lab-scale tests were conducted together with a more mechanistic investigation on how the contaminants were removed. By integrating hydrophobic organic chains with low-cost hydrophilic flocculant matrixes, our biomimetic flocculants achieved a 1.4–9.5 times removal of all detected dissolved PAHs and HMs, while enhancing the removal of a wide-spectrum of particulate and colloidal contaminants, compared to existing SCMs. Ecotoxicity, as indicated by newborn Daphnia magna as experimental organisms, was reduced from “acute toxicity” of the original runoff sample (toxic unit of ∼2.6) to “non-toxicity” (toxic unit < 0.4) of the treated water. The improved performance is attributed to the protein-folding-like features of the bioinspired flocculants providing: (i) stronger binding to PAHs (via hydrophobic association) and HMs (via coordination), and (ii) the ability of spontaneous aggregation. The bio-inspired approach in this work holds strong promise as an alternative or supplementary component in SCM systems, and is expected to contribute to sustainable water management practices in relation to SDGs.

Strategies, Research Priorities, and Challenges for the Exploration of Space Beyond Low Earth Orbit

Abstract NASA's recent emphasis on human exploration of the Moon and, ultimately, Mars necessitates a transition from a focus of its research in the biological sciences from Low Earth Orbit (LEO) to platforms beyond LEO. Fundamental research questions need to be addressed to enable humans to thrive in deep space. Work beyond LEO necessitates a shift in technology and the utilization of organisms in autonomous experiments, especially in the near term. The Beyond LEO Instrumentation &amp; Science Series Science Working Group (BLISS-SWG) was established to provide NASA's Space Biology Program input on its strategy for developing research priorities and tools for exploration beyond LEO. Here, we present an abridged version of the first annual report of the BLISS-SWG, which is publicly available on the NASA Technical Reports Server. Seven priority areas and pertinent research questions were identified for research beyond LEO in the coming 2–5 years. Appropriate experimental organisms and technology development needs for research addressing these questions are summarized. The BLISS-SWG aims for this review to serve as a resource for the space biology and science and engineering communities as they develop research to understand risks and mitigation strategies for deep-space stressors on human crew, plants, and their microbiomes.

The combined effects of polystyrene nanoplastics with nickel on oxidative stress and related toxic effects to earthworms from individual and cellular perspectives

Nanoplastics may adsorb other pollutants in the environment due to their high specific surface area and small size. We used earthworms as experimental organisms to evaluate the ecotoxicity of NPs and Ni combined pollution at the individual and cellular levels. The results showed that when only 20 mg/L Ni2+ was added to the combined pollution system, the antioxidant system of earthworm coelomocytes was destroyed to a certain extent, the ROS level increased, the cell viability decreased significantly, and the redox balance was destroyed. With the introduction of PS-NPs and the increase of concentration, the oxidative damage in the coelomocytes of earthworms gradually increased, and finally tended to be stable when the maximum concentration of 50 mg/L PS-NPs and Ni were exposed together. At the animal level, the activities of CAT and SOD decreased within 28 days of exposure, and the combined pollution showed a synergistic effect. At the same time, it promoted the synthesis of GST in earthworms, improved their detoxification ability and reduced oxidative damage. The changes of T-AOC and MDA showed that the combined pollution caused the accumulation of ROS and caused more serious toxicological effects. With the increase of exposure time, the antioxidant system of earthworms was continuously destroyed, and the oxidative damage was serious, which induced more serious lipid peroxidation and caused the damage of earthworm body wall structure.

The potential of plant action potentials

The mechanism underlying action potentials is routinely used to explicate the mechanistic model of explanation in the philosophy of science. However, characterisations of action potentials often fixate on neurons, mentioning plant cells in passing or ignoring them entirely. The plant sciences are also prone to neglecting non-neuronal action potentials and their role in plant biology. This oversight is significant because plant action potentials bear instructive similarities to those generated by neurons. This paper helps correct the imbalance in representations of action potentials by offering an overview of the mechanism for plant action potentials and highlighting their similarity to those in neurons. Furthermore, it affirms the role of plant action potentials in discovering the evolution and function of mechanisms of action potentials more broadly. We stress the potential of plants for producing generalisations about action potentials and the possible role of plants as experimental organisms.

A minimally invasive procedure for blood extraction from Xenopus laevis allows follow up studies without euthanasia

ABSTRACT Blood extraction is extremely important for the development of scientific research; however, the existing methods for amphibian´s blood sampling are invasive, mainly leading to the euthanasia of the animal. Therefore, less intrusive methods that allow the obtention of multiple samples from the same individual, are needed as an alternative to the common methods available. Hence, the aim of this study was to propose a minimally invasive method for obtaining blood from the hind leg of Xenopus laevis, that allows continuous sampling without compromising the wellbeing of the organisms. With this method, it was possible to extract blood and plasma from adults and juveniles, and the amount of sample was enough to perform biochemical and molecular assays to assess the viability of the blood. The results also revealed that this method is a convenient alternative to obtain blood without affecting the welfare of the experimental organisms, avoiding the cull of the animals, and the samples are viable for their use in follow up studies.

Larval T Cells Are Functionally Distinct from Adult T Cells in Xenopus laevis.

The amphibian Xenopus laevis tadpole provides a unique comparative experimental organism for investigating the roles of innate-like T (iT) cells in tolerogenic immunity during early development. Unlike mammals and adult frogs, where conventional T cells are dominant, tadpoles rely mostly on several prominent distinct subsets of iT cells interacting with cognate nonpolymorphic MHC class I-like molecules. In the present study, to investigate whole T cell responsiveness ontogenesis in X. laevis, we determined in tadpoles and adult frogs the capacity of splenic T cells to proliferate invivo upon infection with two different pathogens, ranavirus FV3 and Mycobacterium marinum, as well as invitro upon PHA stimulation using the thymidine analogous 5-ethynyl-2'-deoxyuridine and flow cytometry. We also analyzed by RT-quantitative PCR T cell responsiveness upon PHA stimulation. In vivo tadpole splenic T cells showed limited capacity to proliferate, whereas the invitro proliferation rate was higher than adult T cells. Gene markers for T cell activation and immediate-early genes induced upon TCR activation were upregulated with similar kinetics in tadpole and adult splenocytes. However, the tadpole T cell signature included a lower amplitude in the TCR signaling, which is a hallmark of mammalian memory-like T cells and iT or "preset" T cells. This study suggests that reminiscent of mammalian neonatal T cells, tadpole T cells are functionally different from their adult counterpart.

A genetically encoded sensor for visualizing leukotriene B4 gradients in vivo

Leukotriene B4 (LTB4) is a potent lipid chemoattractant driving inflammatory responses during host defense, allergy, autoimmune and metabolic diseases. Gradients of LTB4 orchestrate leukocyte recruitment and swarming to sites of tissue damage and infection. How LTB4 gradients form and spread in live tissues to regulate these processes remains largely elusive due to the lack of suitable tools for monitoring LTB4 levels in vivo. Here, we develop GEM-LTB4, a genetically encoded green fluorescent LTB4 biosensor based on the human G-protein-coupled receptor BLT1. GEM-LTB4 shows high sensitivity, specificity and a robust fluorescence increase in response to LTB4 without affecting downstream signaling pathways. We use GEM-LTB4 to measure ex vivo LTB4 production of murine neutrophils. Transgenic expression of GEM-LTB4 in zebrafish allows the real-time visualization of both exogenously applied and endogenously produced LTB4 gradients. GEM-LTB4 thus serves as a broadly applicable tool for analyzing LTB4 dynamics in various experimental systems and model organisms.

Nonhuman Primates in Public Health: Between Biological Standardization, Conservation and Care

By the mid-1960s, nonhuman primates had become key experimental organisms for vaccine development and testing, and was seen by many scientists as important for the future success of this field as well as other biomedical undertakings. A major hindrance to expanding the use of nonhuman primates was the dependency on wild-captured animals. In addition to unreliable access and poor animal health, procurement of wild primates involved the circulation of infectious diseases and thus also public health hazards. This paper traces how the World Health Organization (WHO) became involved in the issue of primate supply, and shows how by the late 1960s concerns for vaccine development and the conservation of wildlife began to converge. How did the WHO navigate public health and animal health? What characterized the response and with what implications for humans and animals? The paper explores how technical standards of care were central to managing the conflicting concerns of animal and human health, biological standardization, and conservation. While the WHO’s main aim was to prevent public health risks, I argue that imposing new standards of care implied establishing new hierarchies of humans and animals, and cultures of care.

BugTracker: Software for Tracking and Measuring Arthropod Activity

The automated video tracking of the activity/movement of an experimental organism is essential for reliable, repeatable quantitative analyses in behavioral ecology and also in other disciplines. There are only some open-access, open-source automated tracking software applications that can track unmarked organisms. Moreover, several of these software applications are substantially affected by brightness and differences in the lighting conditions of the video recording. Our Python-based software, called BugTracker, uses the latest innovations in computer vision technologies to solve these problems. By analyzing videos with considerably different lighting conditions with BugTracker and other available software, we demonstrate that our software could reliably track the studied organisms of any size and speed. Additionally, the results provide accurate measures of the organism’s movements. BugTracker is the most reliable currently available, easy-to-use, and automated tracking software compatible with the Windows, Linux, and MacOS operating systems.

Milk Exosomes: Next-Generation Agents for Delivery of Anticancer Drugs and Therapeutic Nucleic Acids.

Exosomes are nanovesicles 40-120 nm in diameter secreted by almost all cell types and providing humoral intercellular interactions. Given the natural origin and high biocompatibility, the potential for loading various anticancer molecules and therapeutic nucleic acids inside, and the surface modification possibility for targeted delivery, exosomes are considered to be a promising means of delivery to cell cultures and experimental animal organisms. Milk is a unique natural source of exosomes available in semi-preparative and preparative quantities. Milk exosomes are highly resistant to the harsh conditions of the gastrointestinal tract. In vitro studies have demonstrated that milk exosomes have an affinity to epithelial cells, are digested by cells by endocytosis mechanism, and can be used for oral delivery. With milk exosome membranes containing hydrophilic and hydrophobic components, exosomes can be loaded with hydrophilic and lipophilic drugs. This review covers a number of scalable protocols for isolating and purifying exosomes from human, cow, and horse milk. Additionally, it considers passive and active methods for drug loading into exosomes, as well as methods for modifying and functionalizing the surface of milk exosomes with specific molecules for more efficient and specific delivery to target cells. In addition, the review considers various approaches to visualize exosomes and determine cellular localization and bio-distribution of loaded drug molecules in tissues. In conclusion, we outline new challenges for studying milk exosomes, a new generation of targeted delivery agents.