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This article explores the potential of gene editing in the marine algae Neopyropia yezoensis to improve breeding techniques. The study successfully edited a target gene using the CRISPR/Cas9 system, creating gene knockout mutants. This breakthrough paves the way for molecular breeding in N. yezoensis and positions it as a potential model species for marine algae research. The document also discusses the use of P2A as a connector to enhance the efficiency of resistance enrichment screening in gene editing. This advancement in macroalgal gene editing methodologies has implications for precision breeding and the economic seaweed industry. The article acknowledges the contributions of various individuals and organizations to the research. [Extracted from the article]

Insects are intentionally introduced to various regions out of their native ranges to perform fundamental functions, such as pest control, and some keep dispersing from introduction sites to become cosmopolitan and even invasive. The African horned dung beetle, Euoniticellus intermedius (Reiche) (Coleoptera: Scarabaeidae), has been intentionally introduced on multiple continents to bury cattle dung and control livestock pests, but has naturally dispersed and became very abundant at various latitudes and elevations out of its native and original introduction ranges. This beetle has been considered invasive, but there is no direct evidence of its effects on displacing native species. As it is highly fecund, E. intermedius has been an important model in experimental studies performed in nature and in the laboratory in multiple fields. In evolutionary biology, it serves as a model for sexual selection, given the sexual dimorphism characterized by the presence of a horn in males which is correlated with individual condition and strength, and which is absent in females. In ecotoxicology, it has been studied regarding physiological mechanisms of responses to contaminants, population declines, and evolutionary responses to challenging toxic conditions. Given its importance in burying dung in cattle pastures, experiments have also determined environmental conditions that limit this ecological function. Despite being unique in its tolerance to a wide variety of stressors and environments, this species is sensitive to current conditions of global change, including warming and pollution. We identify the most promising questions to be solved in physiology, ecology, and evolution, for which E. intermedius would be an ideal study system. [ABSTRACT FROM AUTHOR]

Plants or tissues can be regenerated through various pathways. Like animal regeneration, cell totipotency and pluripotency are the molecular basis of plant regeneration. Detailed systematic studies on Arabidopsis thaliana gradually unravel the fundamental mechanisms and principles underlying plant regeneration. Specifically, plant hormones, cell division, epigenetic remodeling, and transcription factors play crucial roles in reprogramming somatic cells and reestablishing meristematic cells. Recent research on basal non-vascular plants and monocot crops has revealed that plant regeneration differs among species, with various plant species using distinct mechanisms and displaying significant differences in regenerative capacity. Conducting multi-omics studies at the single-cell level, tracking plant regeneration processes in real-time, and deciphering the natural variation in regenerative capacity will ultimately help understand the essence of plant regeneration, improve crop regeneration efficiency, and contribute to future crop design. [ABSTRACT FROM AUTHOR]

Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant Tree of Life continues to improve. The intersection of these two research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a model clade. These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis thaliana and the family Brassicaceae. We promote the utility of such a model clade and make suggestions for building global networks to support future studies in the model order Brassicales.

Model species (e.g., granivorous gamebirds, waterfowl, passerines, domesticated rodents) have been used for decades in guideline laboratory tests to generate survival, growth, and reproductive data for prospective ecological risk assessments (ERAs) for birds and mammals, while officially adopted risk assessment schemes for amphibians and reptiles do not exist. There are recognized shortcomings of current in vivo methods as well as uncertainty around the extent to which species with different life histories (e.g., terrestrial amphibians, reptiles, bats) than these commonly used models are protected by existing ERA frameworks. Approaches other than validating additional animal models for testing are being developed, but the incorporation of such new approach methodologies (NAMs) into risk assessment frameworks will require robust validations against in vivo responses. This takes time, and the ability to extrapolate findings from nonanimal studies to organism‐ and population‐level effects in terrestrial wildlife remains weak. Failure to adequately anticipate and predict hazards could have economic and potentially even legal consequences for regulators and product registrants. In order to be able to use fewer animals or replace them altogether in the long term, vertebrate use and whole organism data will be needed to provide data for NAM validation in the short term. Therefore, it is worth investing resources for potential updates to existing standard test guidelines used in the laboratory as well as addressing the need for clear guidance on the conduct of field studies. Herein, we review the potential for improving standard in vivo test methods and for advancing the use of field studies in wildlife risk assessment, as these tools will be needed in the foreseeable future. Integr Environ Assess Manag 2024;20:699–724. © 2023 His Majesty the King in Right of Canada and The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC). Reproduced with the permission of the Minister of Environment and Climate Change Canada. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA. Key Points: Improving current approaches for laboratory animal and field effects assessment methods and simultaneously evaluating how to efficiently reduce the numbers of test subjects for the long term are worthy investments of resources.As in vivo animal testing will be required in some form in the near future, it is worth revisiting updates to standard test guidelines to address shortcomings.Clear regulatory guidance is required for field study design and conduct.It is important to fill critical knowledge gaps on the sensitivity of terrestrial amphibians, reptiles, and bats to environmental contaminants compared to current animal models and if necessary validate alternative methods for toxicological effects assesment pertaining to these taxa. [ABSTRACT FROM AUTHOR]

The use of wood distillate (WD) is emerging as a valuable strategy for protecting horticultural crops from the oxidizing effects of ozone (O3). To fully understand its effectiveness, extensive testing on different plant species is needed. As a viable interim measure, an assessment of WD efficacy in model plants can be made until species-specific results become available. The aim of this study is to evaluate the ability of WD to protect the ozone-sensitive tobacco plant (Nicotiana tabacum L.) BelW3 from the oxidizing effects of O3, using the ozone-resistant tobacco plant BelB as a benchmark. The protective effect was evaluated during treatment applications and three weeks after these were completed. Ten BelW3 and five BelB plants were grown just outside Parma from June to October 2023, a period when average maximum O3 concentrations were at least 120 ppb. Starting from July, five BelW3 plants were sprayed weekly with WD at 0.2% for two months. Morphometric and photosynthetic measurements were then taken after six and 11 weeks from the beginning of treatments and three weeks after the end to assess protection persistence (if any). BelW3 showed a significant effect of O3 compared to BelB plants for both morphometric and photosynthetic measurements, exhibiting increased necrotic areas on the leaf blade, reduced number of viable leaves, reduced average plant height, together with reduced chlorophyll content and impaired photosynthetic system functionality. BelW3 plants also showed a significant decrease in the efficiency of parameters related to PSII and PSI when compared to BelB. Wood distillate application, however, successfully mitigated O3 effects on BelW3, as revealed by morphometric and photosynthetic values, which were in line with those observed in BelB. Notably, WD protective effect persisted 3 weeks after treatment cessation, highlighting the short-term protective capacity of the distillate against the oxidative action of O3. [ABSTRACT FROM AUTHOR]

Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the "Project of 1K Medicinal Plant Genome" to decipher their genetic code. However, it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity. Whole genomes of 123 medicinal plants were published until September 2022. These published genome sequences were investigated in this review, covering their classification, research teams, ploidy, medicinal functions, and sequencing strategies. More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes. Diploid species account for a majority of sequenced medicinal plants. The whole genomes of plants in the Poaceae family are the most studied. Almost 40% of the published papers studied species with tonifying, replenishing, and heat-cleaning medicinal effects. Medicinal plants are still in the process of domestication as compared with crops, thereby resulting in unclear genetic backgrounds and the lack of pure lines, thus making their genomes more difficult to complete. In addition, there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome. Herein, a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants. Moreover, whole genome-based biological studies of medicinal plants, including breeding and biosynthesis, were reviewed. We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants. [ABSTRACT FROM AUTHOR]

This study aimed to contribute to the development of an embryo-test using the gastropod Lymnaea stagnalis, identified by the Organization for Economic Co-operation and Development (OECD) as a potential invertebrate test animal model. Together with the Potamopyrgus antipodarum, were the first mollusc models to be included in the organization testing guidelines. The focus was on validating an embryo toxicity test to cover the sensitive embryogenesis phase and on obtaining testing information on all of the model life cycle stages, contributing to close an identified gap within this context. Adhering to OECD guidelines, namely the L. stagnalis reproductive test, the study examined mortality rates, abnormality rates, development, growth, hatching rates, hearth rates, and pre-testing media suitability, during the embryogenesis, and the obtained dataset made available for further studies. Cadmium was chosen as the positive test compound due to its well-studied nature and the model's proven sensitivity to the compound, working as a reference compound for the test development.The data were collected in two 12-day assays under consistent conditions, each using 144 L. stagnalis embryos (

Zooplankton plays a pivotal role in lentic water bodies, linking planktonic primary producers to higher trophic levels and being a cornerstone of the planktonic food web of ponds and lakes. Because of its ease of culture, large size, rich ecology, abundance in northern temperate lakes where limnology is rooted, and the ability to work with clones, Daphnia has, in the last centuries grown to become a key model system in ecology, evolution, and ecotoxicology. Consequently, a vast majority of freshwater zooplankton ecology focuses on the role of Daphnia. While generating essential insights, this has also deviated attention from the broad ecological impact of other zooplankton. Here, we emphasize how other zooplankton taxa have an important impact in nature - often in qualitatively different ways than Daphnia. We illustrate this point by focusing on two key zooplankton functions (herbivory and stoichiometry) and suggest research to capitalize on the success story of mechanistic ecological, eco-evolutionary, and genomic Daphnia work to develop a richer set of model organisms. We currently have the tools to do so and integrating mechanistic insights in multispecies settings would foster a better understanding of the rich diversity and ecology of freshwater zooplankton. [ABSTRACT FROM AUTHOR]

The use of wood distillate (WD) is emerging as a valuable strategy for protecting horticultural crops from the oxidizing effects of ozone (O3). To fully understand its effectiveness, extensive testing on different plant species is needed. As a viable interim measure, an assessment of WD efficacy in model plants can be made until species-specific results become available. The aim of this study is to evaluate the ability of WD to protect the ozone-sensitive tobacco plant (Nicotiana tabacum L.) BelW3 from the oxidizing effects of O3, using the ozone-resistant tobacco plant BelB as a benchmark. The protective effect was evaluated during treatment applications and three weeks after these were completed. Ten BelW3 and five BelB plants were grown just outside Parma from June to October 2023, a period when average maximum O3 concentrations were at least 120 ppb. Starting from July, five BelW3 plants were sprayed weekly with WD at 0.2% for two months. Morphometric and photosynthetic measurements were then taken after six and 11 weeks from the beginning of treatments and three weeks after the end to assess protection persistence (if any). BelW3 showed a significant effect of O3 compared to BelB plants for both morphometric and photosynthetic measurements, exhibiting increased necrotic areas on the leaf blade, reduced number of viable leaves, reduced average plant height, together with reduced chlorophyll content and impaired photosynthetic system functionality. BelW3 plants also showed a significant decrease in the efficiency of parameters related to PSII and PSI when compared to BelB. Wood distillate application, however, successfully mitigated O3 effects on BelW3, as revealed by morphometric and photosynthetic values, which were in line with those observed in BelB. Notably, WD protective effect persisted 3 weeks after treatment cessation, highlighting the short-term protective capacity of the distillate against the oxidative action of O3.

The goal of PrecisionTox is to overcome conceptual barriers to replacing traditional mammalian chemical safety testing by accelerating the discovery of evolutionarily conserved toxicity pathways that are shared by descent among humans and more distantly related animals. An international consortium is systematically testing the toxicological effects of a diverse set of chemicals on a suite of five model species comprising fruit flies, nematodes, water fleas, and embryos of clawed frogs and zebrafish along with human cell lines. Multiple forms of omics and comparative toxicology data are integrated to map the evolutionary origins of biomolecular interactions that are predictive of adverse health effects, to major branches of the animal phylogeny. These conserved elements of adverse outcome pathways (AOPs) and their biomarkers are expected to provide mechanistic insight useful for regulating groups of chemicals based on their shared modes of action. PrecisionTox also aims to quantify risk variation within populations by recognizing susceptibility as a heritable trait that varies with genetic diversity. This initiative incorporates legal experts and collaborates with risk managers to address specific needs within European chemicals legislation, including the uptake of new approach methodologies (NAMs) for setting precise regulatory limits on toxic chemicals. [Display omitted] • PrecisionTox is funded by the EU's Horizon 2020 programme until the year 2026. • Conserved toxicity pathways will be identified across five model organisms and humans. • Artificial intelligence will reveal adverse outcome pathways and their biomarkers. • Quantitative genetics is used to examine susceptibility to toxicity as a variable trait. • Collaboration with policy makers facilitates use of biomarkers for safety assessment. [ABSTRACT FROM AUTHOR]

Annual killifish live in temporary pools which completely lose water during the dry season. They bury their eggs in the muddy bottom where they stay through the entire dry season. The development of killifish embryos involves three strictly defined stages, where the embryo may go dormant and stop developmental progression. The system of the three facultative diapauses — diapause I, II, and III — was described in the 1970s and remained supported until now. Here, we report on the potential of the embryos of an African killifish species Nothobranchius furzeri Jubb to enter an additional developmental stasis occurring in between the stages defined for the diapause II and III. The stasis manifests as a full developmental halt in a stage previously regarded as non-diapausing or a markedly slowed down developmental rate. It occurs under usual laboratory incubation conditions, and the embryos that entered the stasis are capable of normal hatching after they exit the dormancy and complete their development. The aim of the study is to inform on the increased, cryptic complexity of the killifish diapause system while we discuss the possible reasons why the stasis, arguably occurring with some regularity, remained unnoticed for so long. [ABSTRACT FROM AUTHOR]

Since the banning of tributyltin, the addition of inorganic (metal oxides) and organic (pesticides, herbicides) biocides in antifouling paint has represented an unavoidable step to counteract biofouling and the resulting biodeterioration of submerged surfaces. Therefore, the development of new methods that balance antifouling efficacy with environmental impact has become a topic of great importance. Among several proposed strategies, natural extracts may represent one of the most suitable alternatives to the widely used toxic biocides. Posidonia oceanica is one of the most representative organisms of the Mediterranean Sea and contains hundreds of bioactive compounds. In this study, we prepared, characterized, and assessed a hydroalcoholic extract of P. oceanica and then compared it to three model species. Together, these four species belong to relevant groups of biofoulers: bacteria (Aliivibrio fischeri), diatoms (Phaeodactylum tricornutum), and serpulid polychaetes (Ficopomatus enigmaticus). We also added the same P. oceanica extract to a PDMS-based coating formula. We tested this coating agent with Navicula salinicola and Ficopomatus enigmaticus to evaluate both its biocidal performance and its antifouling properties. Our results indicate that our P. oceanica extract provides suitable levels of protection against all the tested organisms and significantly reduces adhesion of N. salinicola cells and facilitates their release in low-intensity waterflows. [ABSTRACT FROM AUTHOR]

Despite research efforts toward improving crop photosynthetic energy conversion efficiencies over the past 40 years, photosynthetic efficiencies remain far from their theoretical maxima. A major challenge has been that plant photosynthesis is a complex process, controlled by many underlying genetic factors and highly dynamic in response to short‐term environmental changes. Recent approaches to improving photosynthesis involved model‐based identification of the bottlenecks in photosynthesis followed by their genetic modification (GM). While these approaches were successful and inspirational, their dependency on the use of GM techniques may restrict their implementation in some jurisdictions. We therefore suggest greater research focus on a different, yet complementary, approach to improving photosynthetic efficiency: the exploration and exploitation of natural genetic variation in photosynthesis. A substantial improvement in phenotyping and genotyping technology over the past decade has highlighted natural variation in photosynthetic sub‐traits for crop and model species. However, a comprehensive understanding of all the factors responsible for photosynthetic limitations is still lacking. We therefore propose the use of high photosynthetic capacity species as models for the exploration of the physiological and genetic basis of high photosynthetic efficiency. While most high photosynthetic capacity species are not suitable as models due to complex genetics and evolutionary distance from crops, we have identified Brassicaceae species Hirschfeldia incana (L.) Lagr.‐Foss as a promising candidate. In this perspective paper, we describe and advocate the use of H. incana as a model for the exploration of high maximum CO2 assimilation rates (Pmax) found in some C3 species. We describe the basic biology and evolutionary history of the species and report preliminary data on its photosynthetic characteristics. Our findings suggest H. incana is an excellent model species for studies aiming at understanding natural genetic variation in photosynthetic efficiency. [ABSTRACT FROM AUTHOR]

Abstract Despite research efforts toward improving crop photosynthetic energy conversion efficiencies over the past 40 years, photosynthetic efficiencies remain far from their theoretical maxima. A major challenge has been that plant photosynthesis is a complex process, controlled by many underlying genetic factors and highly dynamic in response to short‐term environmental changes. Recent approaches to improving photosynthesis involved model‐based identification of the bottlenecks in photosynthesis followed by their genetic modification (GM). While these approaches were successful and inspirational, their dependency on the use of GM techniques may restrict their implementation in some jurisdictions. We therefore suggest greater research focus on a different, yet complementary, approach to improving photosynthetic efficiency: the exploration and exploitation of natural genetic variation in photosynthesis. A substantial improvement in phenotyping and genotyping technology over the past decade has highlighted natural variation in photosynthetic sub‐traits for crop and model species. However, a comprehensive understanding of all the factors responsible for photosynthetic limitations is still lacking. We therefore propose the use of high photosynthetic capacity species as models for the exploration of the physiological and genetic basis of high photosynthetic efficiency. While most high photosynthetic capacity species are not suitable as models due to complex genetics and evolutionary distance from crops, we have identified Brassicaceae species Hirschfeldia incana (L.) Lagr.‐Foss as a promising candidate. In this perspective paper, we describe and advocate the use of H. incana as a model for the exploration of high maximum CO2 assimilation rates (Pmax) found in some C3 species. We describe the basic biology and evolutionary history of the species and report preliminary data on its photosynthetic characteristics. Our findings suggest H. incana is an excellent model species for studies aiming at understanding natural genetic variation in photosynthetic efficiency.

SUMMARY: Photosynthesis is a key process in sustaining plant and human life. Improving the photosynthetic capacity of agricultural crops is an attractive means to increase their yields. While the core mechanisms of photosynthesis are highly conserved in C3 plants, these mechanisms are very flexible, allowing considerable diversity in photosynthetic properties. Among this diversity is the maintenance of high photosynthetic light‐use efficiency at high irradiance as identified in a small number of exceptional C3 species. Hirschfeldia incana, a member of the Brassicaceae family, is such an exceptional species, and because it is easy to grow, it is an excellent model for studying the genetic and physiological basis of this trait. Here, we present a reference genome of H. incana and confirm its high photosynthetic light‐use efficiency. While H. incana has the highest photosynthetic rates found so far in the Brassicaceae, the light‐saturated assimilation rates of closely related Brassica rapa and Brassica nigra are also high. The H. incana genome has extensively diversified from that of B. rapa and B. nigra through large chromosomal rearrangements, species‐specific transposon activity, and differential retention of duplicated genes. Duplicated genes in H. incana, B. rapa, and B. nigra that are involved in photosynthesis and/or photoprotection show a positive correlation between copy number and gene expression, providing leads into the mechanisms underlying the high photosynthetic efficiency of these species. Our work demonstrates that the H. incana genome serves as a valuable resource for studying the evolution of high photosynthetic light‐use efficiency and enhancing photosynthetic rates in crop species. Significance Statement: Hirschfeldia incana is a diploid, wild species, closely related to Brassica crops, which displays remarkably high photosynthesis rates at high irradiance, a desirable trait to improve in crops to increase yield. We propose H. incana as an attractive high‐photosynthesis model species and present the reference genome sequence as a valuable resource for studying the evolution, genetics, and physiology of high photosynthetic light‐use efficiency at high irradiances. [ABSTRACT FROM AUTHOR]

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Summary: Comparative analyses of growth‐regulatory mechanisms between Arabidopsis and maize revealed that even when the gene space is conserved, the translation of knowledge from model species to crops is not trivial. Based on these insights, we formulate future opportunities to improve the interpretation of curiosity‐driven research towards crop improvement. [ABSTRACT FROM AUTHOR]

Toxicology is traditionally divided between human and eco-toxicology. In the shared pursuit of environmental health, this separation does not account for discoveries made in the comparative studies of animal genomes. Here, we provide evidence on the feasibility of understanding the health impact of chemicals on all animals, including ecological keystone species and humans, based on a significant number of conserved genes and their functional associations to health-related outcomes across much of animal diversity. We test four conditions to understand the value of comparative genomics data to inform mechanism-based human and environmental hazard assessment: (1) genes that are most fundamental for health evolved early during animal evolution; (2) the molecular functions of pathways are better conserved among distantly related species than the individual genes that are members of these pathways; (3) the most conserved pathways among animals are those that cause adverse health outcomes when disrupted; (4) gene sets that serve as molecular signatures of biological processes or disease-states are largely enriched by evolutionarily conserved genes across the animal phylogeny. The concept of homology is applied in a comparative analysis of gene families and pathways among invertebrate and vertebrate species compared with humans. Results show that over 70% of gene families associated with disease are shared among the greatest variety of animal species through evolution. Pathway conservation between invertebrates and humans is based on the degree of conservation within vertebrates and the number of interacting genes within the human network. Human gene sets that already serve as biomarkers are enriched by evolutionarily conserved genes across the animal phylogeny. By implementing a comparative method for chemical hazard assessment, human and eco-toxicology converge towards a more holistic and mechanistic understanding of toxicity disrupting biological processes that are important for health and shared among animals (including humans).

Although some authors previously questioned the circumscription of Nicotiana benthamiana , it has never been treated taxonomically as more than a single widespread, variable species. A recent study employing phylogenetic and population genetic analyses has demonstrated that N. benthamiana comprises five species that are geographically and morphologically distinct. Here, we describe four new species in the N. benthamiana complex, namely, N. bilybara M.W.Chase & Christenh., N. candelabra M.W.Chase & Christenh., N. rupestris M.W.Chase & Christenh. and N. scopulorum M.W.Chase & Christenh., and illustrate all five. We provide descriptions, a diagnostic key and a table of morphological characters distinguishing these closely related species. The major morphological feature that distinguishes N. benthamiana from the other four species is its petiolate leaves that become sessile only near the apex of the inflorescence; N. candelabra is distinct in its bifacial branching, N. bilybara in its commonly winged petiole with an auriculate base, N. rupestris in the leafy apices of its calyx lobes, and N. scopulorum is the least morphologically divergent species, conforming most closely to the general description of the N. benthamiana species complex. A recent study employing phylogenetic and population genetic analyses has demonstrated that the important model plant, Nicotiana benthamiana , is not a single species but instead comprises five species that are geographically and morphologically distinct. Here, we describe four new species in the N. benthamiana complex and illustrate all five. [ABSTRACT FROM AUTHOR]

Apomixis, or asexual reproduction by seed, represents an easy shortcut for life cycle renewal based on maternal embryo production without ploidy reduction (meiosis) and ploidy restitution (syngamy). Although the first studies officially published on this topic in scientific journals date back to the early 1930s, the identification and introduction of genes involved in asexual reproduction in species of agronomic interest still represent a major challenge. Through a bibliometric analysis of the research programs implemented in apomixis over the last 40 years, the present study was aimed to discuss not only the main findings achieved but also the investigational methods and model species used. We split the critical survey of the most cited original articles into pregenomic and genomic eras to identify potential trends and depict scenarios that have emerged in the scientific community working on apomixis, as well as to determine any correlation between the exponential increase in acquired basic knowledge and the development of advanced analytical technologies. This review found a substantial stagnation in the use of the same model species, with few exceptions, for at least 40 years. In contrast, the development of new molecular techniques, genomic platforms, and repositories has directly affected the approaches used in research, which has been directed toward an increasingly focused study of the genetic and epigenetic determinants of apomixis. [ABSTRACT FROM AUTHOR]

Apomixis, or asexual reproduction by seed, represents an easy shortcut for life cycle renewal based on maternal embryo production without ploidy reduction (meiosis) and ploidy restitution (syngamy). Although the first studies officially published on this topic in scientific journals date back to the early 1930s, the identification and introduction of genes involved in asexual reproduction in species of agronomic interest still represent a major challenge. Through a bibliometric analysis of the research programs implemented in apomixis over the last 40 years, the present study was aimed to discuss not only the main findings achieved but also the investigational methods and model species used. We split the critical survey of the most cited original articles into pregenomic and genomic eras to identify potential trends and depict scenarios that have emerged in the scientific community working on apomixis, as well as to determine any correlation between the exponential increase in acquired basic knowledge and the development of advanced analytical technologies. This review found a substantial stagnation in the use of the same model species, with few exceptions, for at least 40 years. In contrast, the development of new molecular techniques, genomic platforms, and repositories has directly affected the approaches used in research, which has been directed toward an increasingly focused study of the genetic and epigenetic determinants of apomixis.

The most widespread and numerous inland fish in the world is likely the mosquitofish (Gambusia affinis and G. holbrooki, Poeciliidae). Much has been written about the basic biology, the current distribution and the negative impacts of non‐native populations of mosquitofish. Here, we instead review the relationship of humanity with mosquitofish. First, we review the early literature on the species and aim to resolve its path towards becoming the globally dominant fish for biological control of mosquitoes. We identify the initial advocates of mosquitofish use, we examine the reasons behind their advocacy, and we document the spread of their viewpoints into and from the globally foundational mosquito control texts. Second, we identify the people and institutions that facilitated early international translocations of mosquitofish, including, among others, David Starr Jordan, the Rockefeller Foundation and the International Red Cross. Third, we discuss the reduction in mosquitofish translocation and use during and after WWII, initially stemming from the discovery and use of other methods, like DDT and later from a recognition of the negative ecological consequences of non‐native mosquitofish populations. Fourth, we propose that the future utility of mosquitofish is largely in its value as a model study organism. We provide an overview of the contributions mosquitofish have made to some major fields in biology. Finally, we suggest that the value of mosquitofish as a model system should increase into the future, behind a momentum of research advances, and as human‐mediated range expansion will permit access to mosquitofish by yet greater numbers of biologists worldwide. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The Asteraceae family is the largest and most diversified family of the Angiosperms, characterized by the presence of numerous clustered inflorescences, which have the appearance of a single compound flower. It is estimated that this family represents around 10% of all flowered species, with a great biodiversity, covering all environments on the planet, except Antarctica. Also, it includes economically important crops, such as lettuce, sunflower, and chrysanthemum; wild flowers; herbs, and several species that produce molecules with pharmacological properties. Nevertheless, the biotechnological improvement of this family is limited to a few species and their genetic transformation was achieved later than in other plant families. Lettuce (Lactuca sativa L.) is a model species in molecular biology and plant biotechnology that has easily adapted to tissue culture, with efficient shoot regeneration from different tissues, organs, cells, and protoplasts. Due to this plasticity, it was possible to obtain transgenic plants tolerant to biotic or abiotic stresses as well as for the production of commercially interesting molecules (molecular farming). These advances, together with the complete sequencing of lettuce genome allowed the rapid adoption of gene editing using the CRISPR system. On the other hand, sunflower (Helianthus annuus L.) is a species that for years was considered recalcitrant to in vitro culture. Although this difficulty was overcome and some publications were made on sunflower genetic transformation, until now there is no transgenic variety commercialized or authorized for cultivation. In this article, we review similarities (such as avoiding the utilization of the CaMV35S promoter in transformation vectors) and differences (such as transformation efficiency) in the state of the art of genetic transformation techniques performed in these two species. [ABSTRACT FROM AUTHOR]

The Asteraceae family is the largest and most diversified family of the Angiosperms, characterized by the presence of numerous clustered inflorescences, which have the appearance of a single compound flower. It is estimated that this family represents around 10% of all flowered species, with a great biodiversity, covering all environments on the planet, except Antarctica. Also, it includes economically important crops, such as lettuce, sunflower, and chrysanthemum; wild flowers; herbs, and several species that produce molecules with pharmacological properties. Nevertheless, the biotechnological improvement of this family is limited to a few species and their genetic transformation was achieved later than in other plant families. Lettuce (Lactuca sativa L.) is a model species in molecular biology and plant biotechnology that has easily adapted to tissue culture, with efficient shoot regeneration from different tissues, organs, cells, and protoplasts. Due to this plasticity, it was possible to obtain transgenic plants tolerant to biotic or abiotic stresses as well as for the production of commercially interesting molecules (molecular farming). These advances, together with the complete sequencing of lettuce genome allowed the rapid adoption of gene editing using the CRISPR system. On the other hand, sunflower (Helianthus annuus L.) is a species that for years was considered recalcitrant to in vitro culture. Although this difficulty was overcome and some publications were made on sunflower genetic transformation, until now there is no transgenic variety commercialized or authorized for cultivation. In this article, we review similarities (such as avoiding the utilization of the CaMV35S promoter in transformation vectors) and differences (such as transformation efficiency) in the state of the art of genetic transformation techniques performed in these two species.

Cryopreservation of sperm is an important tool for the conservation of threatened species. Many species of reptile are under considerable threat of extinction and there has been limited investigation of sperm cryopreservation in this taxonomic group. We performed a comparative test of toxicity to sperm of six commonly used cryoprotective agents (CPAs) at three concentrations (5%, 10%, 20%) from the Louisiana pinesnake, Pituophis ruthveni (n = 11), and the closely related bullsnake, Pituophis cantenifer (n = 8). Our objective was to determine the general toxicity of CPAs for cryopreservation in snakes and the cryoprotective ability of CPAs for sperm from the endangered Louisiana pinesnake. We conducted three experiments to: 1) evaluate the short-term in vitro toxicity of common CPAs in two closely related snake species, 2) determine the effectiveness of cryoprotectants for freezing and thawing semen in the Louisiana pinesnake, and 3) test the possible reduction in toxic effects of individual CPAs on semen of the Louisiana pinesnake by combining two of them. We used measures of motility including total motility, forward motility, and forward progressive motility index to characterize toxic effects and cryoprotective ability of each CPA. The results of our three experiments provide several important findings: 1) sperm of the bullsnake and Louisiana pinesnake responded differently to CPAs, 2) few CPAs provided any cryoprotection, as measured by percent recovered motility, in Louisiana pinesnakes, and 3) using mixtures of CPAs did not reduce toxicity relative to the best performing CPA on its own. Motility was best maintained at a concentration of 5% for CPAs tested; however, cryoprotection was best achieved with glycerol at 20% followed by DMA and DMF at 10%. These results provide further insight into the challenges faced by researchers attempting to cryopreserve sperm from snakes. Further comparative studies are required to determine the generality of cryopreservation methods in reptiles and suggest caution should be taken when developing cryopreservation protocols across species, particularly in snakes. All CPAs tested in this study were permeating CPAs and showed a significant acute toxic effect on motility at concentrations that provided cryoprotection. Future work in snakes might consider additional avenues of cryoprotection and combinations of multiple approaches. • Motility of sperm from two closely-species of snake respond in differ ways to six common cryoprotectant agents. • First successful cryopreservation of sperm from the endangered Louisiana pinesnake. • Mixtures of cryoprotectant agents may not reduce toxic effect on sperm motility in snakes. [ABSTRACT FROM AUTHOR]

Comparative neuroscience is entering the era of big data. New high-throughput methods and data-sharing initiatives have resulted in the availability of large, digital data sets containing many types of data from ever more species. Here, we present a framework for exploiting the new possibilities offered. The multimodality of the data allows vertical translations, which are comparisons of different aspects of brain organization within a single species and across scales. Horizontal translations compare particular aspects of brain organization across species, often by building abstract feature spaces. Combining vertical and horizontal translations allows for more sophisticated comparisons, including relating principles of brain organization across species by contrasting horizontal translations, and for making formal predictions of unobtainable data based on observed results in a model species. [ABSTRACT FROM AUTHOR]

Macrobrachium pantanalense is a recently described endemic shrimp from Pantanal. The species completes its life cycle in freshwater and is used as an ornamental species for freshwater aquaria, as well as a model organism in risk assessment trials of anthropic impacts. However, all risk assessment trials performed to date have used wild specimens. As such, it is paramount to standardize the laboratory culture of M. pantanalense to allow the use of cultured specimens that safeguard the reliability and replicability of trials being performed. The present work evaluated the use of freshwater and different salinity levels (2, 4 and 6) for the larviculture of M. pantanalense, as well as larval stocking densities of 20, 40 and 60 larvae L−1. Six different larval feeding regimes were also evaluated: 100 % newly hatched Artemia nauplii (AN), 100 % wild zooplankton (WZ), 100 % inert diet (ID), 50 % AN + 50 % WZ, 50 % AN + 50 % ID and 50 % WZ + 50 % ID. Larvae of M. pantanalense were able to successfully metamorphose to post larvae (PL) when cultured in freshwater, although a higher % of PL was achieved under a salinity of 4 (25.6 ± 15.0 %). No significant differences were recorded in survival under different stocking densities. The best larval feeding regime tested was 100AN, promoting a higher production of PL (44.3 ± 18.3 %) when compared with other diets. Overall, the larviculture of M. pantanalense can be enhanced by using brackish water instead of freshwater. By employing a moderate larval stocking density (up to 60 larvae L−1) and an easy to use “of-the-shelf” larval live feed (Artemia nauplii) PL of M. pantanalense can be produced in the laboratory. The present findings are a first step towards the development of a production protocol for M. pantanalense in the laboratory to perform risk assessment trials of growing anthropic stressors impacting Pantanal.

There are many limitations when using traditional laboratory species. Limits on variation, may result in limited outcomes, at both the species and individual level, due to different individuals/species having diverse physiological processes, or differing molecular and genetic mechanisms. By using a variety of model species, we will be able to develop creative solutions to biological problems and identify differences of which we were not previously aware. The laboratory mouse has been a suitable model species for various mammalian studies, however most are bred specifically for laboratory research with limited variability due to selective breeding. Marsupial models offer unique research opportunities compared to eutherian models. We believe that there should be an expansion in marsupial model species, and the introduction of the red‐tailed phascogale (Phascogale calura), a dasyurid marsupial, should be one of them. Phascogales are easily managed in captivity, and there are now multiple studies involving their development, reproduction, nutrition, behavior and immune system, which can serve as a baseline for future studies. The addition of the phascogale as a model species will improve future mammalian studies by introducing variability and offer alternate solutions to biological problems, particularly in the areas of genetics, nutrition, immunology, the neuro‐endocrine system, and ageing, due to their semelparous reproductive strategy and hence, subsequent predictive physiology. In this review, we provide information based on existing research on red‐tailed phascogales to support their inclusion as a model species. Highlights: Traditional laboratory species are limited in variation, hence can limit scientific outcomes.Red‐tailed phascogales are semelparous and easily managed in captivity.They offer an alternative animal model to investigate biological problems. [ABSTRACT FROM AUTHOR]

This study aimed to contribute to the development of an embryo-test using the gastropod Lymnaea stagnalis , identified by the Organization for Economic Co-operation and Development (OECD) as a potential invertebrate test animal model. Together with the Potamopyrgus antipodarum , were the first mollusc models to be included in the organization testing guidelines. The focus was on validating an embryo toxicity test to cover the sensitive embryogenesis phase and on obtaining testing information on all of the model life cycle stages, contributing to close an identified gap within this context. Adhering to OECD guidelines, namely the L. stagnalis reproductive test, the study examined mortality rates, abnormality rates, development, growth, hatching rates, hearth rates, and pre-testing media suitability, during the embryogenesis, and the obtained dataset made available for further studies. Cadmium was chosen as the positive test compound due to its well-studied nature and the model's proven sensitivity to the compound, working as a reference compound for the test development. The data were collected in two 12-day assays under consistent conditions, each using 144 L. stagnalis embryos (<24 h old) from 6 egg masses (288 embryos total). Six 48-well microplates were utilized per assay, accommodating five different cadmium concentrations (32, 70, 155, 341, 750 µg/L) and a control group. Recorded parameters encompassed developmental stage, embryo position within the chorion, developmental abnormalities, hatchings, and mortality. Data analysis involved classifying embryos based on developmental stage and position, taking an exploratory approach to define the relevance of the different parameters in the compound hazard assessment during the embryogenesis. Measurements considered embryo area, perimeter, length, height, width, interocular distance, and heart rate. This dataset does not provide treated information but the raw data obtained during the proposed metodological development and toxicity testing process. The purpose of this article is to make the obtained raw data available, clearly defining the acquisition methodology to provide a comparison basis for future or existent works within this context., (© 2024 The Authors. Published by Elsevier Inc.)

Growth rate (GR), esterase activity (EA), membrane potential (MP), and DNA content were measured by flow cytometry to test if this powerful tool could be included in risk assessment and monitoring programs. This study tests a battery of endpoints that were measured on Scenedesmus (Acutodesmus) obliquus as model species, under high levels of injected CO2 to be proposed as biomarkers of effect. New technologies such as carbon capture and storage (CCS) bring positive consequences on CO2 mitigation strategies but also could have negative consequences if a CO2 leakage occurs during injection. Under this scenario, pH might drop down to 4 pH units around the pipe where the leakage happens. The study focus on to ascertain if the endpoints fulfill the requirements such as sensitiveness, be timely and cost‐effective, be easy to measure and interpret, and be nondestructive, valuable attributes in effective biomarkers. CO2 injected at high levels significantly affects the EA, the membrane polarization, as well as GRs. However the DNA content did not shown a clear response under this condition. In conclusion, the GR, the EA, and the MP analyzed by flow cytometry fulfilled the attributes mentioned above and are proposed as biomarkers of effect in CCS monitoring programs. © 2020 International Society for Advancement of Cytometry [ABSTRACT FROM AUTHOR]

N6-methyladenosine (6mA) DNA modification played an important role in epigenetic regulation of gene expression. And the aberrational expression of non-coding genes, as important regular elements of gene expression, was related to many diseases. However, the distribution and potential functions of 6mA modification in non-coding RNA (ncRNA) genes are still unknown. In this study, we analyzed the 6mA distribution of ncRNA genes and compared them with protein-coding genes in four species (Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, and Homo sapiens) using single-molecule real-time (SMRT) sequencing data. The results indicated that the consensus motifs of short nucleotides at 6mA location were highly conserved in four species, and the non-coding gene was less likely to be methylated compared with protein-coding gene. Especially, the 6mA-methylated lncRNA genes were expressed significant lower than genes without methylation in A. thaliana (p = 3.295e-4), D. melanogaster (p = 3.439e-11), and H. sapiens (p = 9.087e-3). The detection and distribution profiling of 6mA modification in ncRNA regions from four species reveal that 6mA modifications may have effects on their expression level.

It is generally accepted that land plants evolved from streptophyte algae. However, there are also many chlorophytes (a sister group of streptophyte algae and land plants) that moved to terrestrial habitats and even resemble mosses. This raises the question of why no land plants evolved from chlorophytes. In order to better understand what enabled streptophyte algae to conquer the land, it is necessary to study the chlorophytes as well. This review will introduce the freshwater filamentous chlorophyte alga Draparnaldia sp. (Chaetophorales, Chlorophyceae) as a model for comparative analyses between these two lineages. It will also focus on current knowledge about the evolution of morphological complexity in chlorophytes versus streptophytes and their respective morphological/behavioural adaptations to semi-terrestrial habitats, and will show why Draparnaldia is needed as a new model system. [ABSTRACT FROM AUTHOR]

Variations between distinct natural markings of freckled hawkfish (Paracirrhites forsteri) could allow in situ identification of individuals from underwater photography. Receiver operating characteristic analysis was used to assess the ability of the Interactive Individual Identification System (I3S) software to assist in discriminating between images of P. forsteri individuals. This study's results show the high discriminant ability of I3S to differentiate between unlike individuals and identify images of the same individual. The ability to use automatic computer‐aided assistance in the study of this species will enable future research to explore behaviour and movements of individuals in the wild. [ABSTRACT FROM AUTHOR]

Octopuses represent interesting model studies for different fields of scientific inquiry. The present study provides a bibliometric analysis on research trends in octopuses biological studies. The analysis was executed from January 1985 to December 2020 including scientific products reported in the Web of Science database. The period of study was split into two blocks (“earlier period” (EP): 1985−2010; “recent period” (RP): 2011−2020) to analyze the evolution of the research topics over time. All publications of interest were identified by using the following query: ((AK = octopus) OR (AB = octopus) OR (TI = octopus)). Data information was converted into an R-data frame using bibliometrix. Octopuses studies appeared in 360 different sources in EP, while they increased to 408 in RP. Sixty countries contributed to the octopuses studies in the EP, while they were 78 in the RP. The number of affiliations also increased between EP and RP, with 835 research centers involved in the EP and 1399 in the RP. In the EP 5 clusters (i.e., “growth and nutrition”, “pollution impact”, “morphology”, “neurobiology”, “biochemistry”) were represented in a thematic map, according to their centrality and density ranking. In the RP the analysis identified 4 clusters (i.e., “growth and nutrition”, “ecology”, “pollution impact”, “genes, behavior, and brain evolution”). The UK with Ireland, and the USA with Canada shared the highest number of publications in the EP, while in the RP, Spain and Portugal were the leading countries. The current data provide significant insight into the evolving trends in octopuses studies.

In the present study, we compared the toxicity and associated chemical characterizations of flowback and produced water (FPW) collected from a single horizontal hydraulically fractured well at different time points during FPW production. Since few studies on whole mixture toxicity related to FPW exist, our aims were to determine both overall toxicity of the FPW mixture in a suite of organisms (Daphnia magna, Lumbriculus variegatus , Danio rerio, and Oncorhynchus mykiss) and also determine if toxicity changes depending on variation in FPW chemical properties as a function of time sampled (1.33, 72, and 228 h FPW samples collected immediately post-well production onset were analyzed in current study). FPW chemical composition was determined via quadra-pole inductively coupled plasma – mass spectrometry/mass spectrometry (ICP-MS/MS), full-scan high performance liquid chromatography/Orbitrap mass spectrometry (HPLC/Orbitrap-MS), and gas chromatography-mass spectrometry (GC-MS). We observed that FPW sampled later in the production process contained higher ion and total dissolved solids concentrations, whereas the highest concentrations of dissolved organic compounds were observed in the earliest FPW sample analyzed. Toxicity associated with FPW exposure was deemed to be species-specific to a certain extent, but general trends revealed the earliest FPW sampled contained highest toxic potential. Accordingly, we theorize that although the saline conditions of FPW are the foremost toxicological drivers to freshwater organisms, dissolved organics associated with FPW significantly contribute to the overall toxicity of exposed organisms. Image 1 • Temporal sampling of Hydraulic Fracturing Flowback and Produced Water (FPW) toxicity. • Earliest FPW samples had highest toxicity amongst most aquatic species examined. • Increases in FPW total dissolved solids occurs as FPW sampling continues. • Organics are highly variable but are generally highest in earlier FPW samples. • Species specific sensitivity to FPW reflects differences in organism biology. [ABSTRACT FROM AUTHOR]

Assembly of publically available next-generation sequence data facilitated the generation of three camarodont echinoid mitogenomes: two for the Green Urchin (Lytechinus variegatus) and one for the Red Urchin (Mesocentrotus franciscanus). The data generated are exploited in a phylogenomic analysis of the superfamily Odontophora, originally proposed for echinoids with tooth supports on the epiphyses of the jaw. The analysis highly supports this taxon and its current subdivision into three families: the Echinometridae, Toxopneustidae, and Strongylocentrotidae. The analysis furthermore implies that historical taxonomic issues between two members of the genus Strongylocentrotus (S. pallidus and S. droebachiensis) may have a genetic basis. The novel mitogenomes for the model species L. variegatus complements the draft genome available for this taxon, one of only three genome-enabled echinoid species. The assembly method applied herein, follows a divide-and-conquer approach that provides for reduced computational requirements and facilitates resolving assembly problems when processing ultra-high coverage next-generation sequence data. • The first mitochondrial genome of the model echinoid Lytechinus variegatus. • Phylogenomic analysis of the echinoid superfamily Odontophora based on complete mitogenomes. • Computational efficient assembly pipeline for processing ultra-high coverage NGS data. [ABSTRACT FROM AUTHOR]

Light pollution is an ever increasing worldwide problem disrupting animal behavior. Artificial light at night (ALAN) has been shown to affect sleep in wild birds. Even cavity-nesting bird species may be affected when sleeping inside their cavity. Correlational studies suggest that light from outside the cavity/nest box, for example from street lights, may affect sleep. We used an experimental design to study to what extent nest boxes shield animals from effects of ALAN on sleep. We recorded individual sleep behavior of free-living great tits (Parusmajor) that were roosting in dark nest boxes and exposed their nest box entrance to ALAN the following night (1.6 lux white LED light; a similar light intensity as was found at nest boxes near street lights). Their behavior was compared to that of control birds sleeping in dark nest boxes on both nights. Our experimental treatment did not affect sleep behavior. Sleep behavior of birds in the control group did not differ from that of individuals in the light treated group. Our results suggest that during winter cavities shield birds from some effects of ALAN. Furthermore, given that effects of ALAN and exposure to artificial light are species-, sex-, and season-dependent, it is important that studies using wild animals quantify individual exposure to light pollution, and be cautious in the interpretation and generalization of the effects, or lack thereof, from light pollution. Rigorous studies are necessary to examine individual light exposure and its consequences in cavity- and open-nesting birds. [ABSTRACT FROM AUTHOR]