Xenopus

Advances in the Xenopus immunome: Diversification, expansion, and contraction

Xenopus is a genus of African clawed frogs including two species, X. tropicalis and X. laevis that are extensively used in experimental biology, immunology, and biomedical studies. The availability of fully sequenced and annotated Xenopus genomes is strengthening genome-wide analyses of gene families and transgenesis to model human diseases. However, inaccuracies in genome annotation for genes involved in the immune system (i.e., immunome) hamper immunogenetic studies. Furthermore, advanced genome technologies (e.g., single-cell and RNA-Seq) rely on well-annotated genomes. The annotation problems of Xenopus immunome include a lack of established orthology across taxa, merged gene models, poor representation in gene pages on Xenbase, misannotated genes and missing gene IDs. The Xenopus Research Resource for Immunobiology in collaboration with Xenbase and a group of investigators are working to resolve these issues in the latest versions of genome browsers. In this review, we summarize the current problems of previously misannotated gene families that we have recently resolved. We also highlight the expansion, contraction, and diversification of previously misannotated gene families.

Tissue-Targeted CRISPR-Cas9-Mediated Genome Editing of Multiple Homeologs in F0-Generation Xenopus laevis Embryos

Xenopus laevis frogs are a powerful developmental model that enables studies combining classical embryology and molecular manipulation. Because of the large embryo size, ease of microinjection, and ability to target tissues through established fate maps, X. laevis has become the predominant amphibian research model. Given that their allotetraploid genome has complicated the generation of gene knockouts, strategies need to be established for efficient mutagenesis of multiple homeologs to evaluate gene function. Here we describe a protocol to use CRISPR-Cas9-mediated genome editing to target either single alleles or multiple alloalleles in F0 X. laevis embryos. A single-guide RNA (sgRNA) is designed to target a specific DNA sequence encoding a critical protein domain. To mutagenize a gene with two alloalleles, the sgRNA is designed against a sequence that is common to both homeologs. This sgRNA, along with the Cas9 protein, is microinjected into the zygote to disrupt the genomic sequences in the whole embryo or into a specific blastomere for tissue-targeted effects. Error-prone repair of CRISPR-Cas9-generated DNA double-strand breaks leads to insertions and deletions creating mosaic gene lesions within the embryos. The genomic DNA isolated from each mosaic F0 embryo is sequenced, and software is applied to assess the nature of the mutations generated and degree of mosaicism. This protocol enables the knockout of genes within the whole embryo or in specific tissues in F0 X. laevis embryos to facilitate the evaluation of resulting phenotypes.

Assays for Apical Constriction Using the Xenopus Model

Apical constriction refers to the active, actomyosin-driven process that reduces apical cell surface area in epithelial cells. Apical constriction is utilized in epithelial morphogenesis during embryonic development in multiple contexts, such as gastrulation, neural tube closure, and organogenesis. Defects in apical constriction can result in congenital birth defects, yet our understanding of the molecular control of apical constriction is relatively limited. To uncover new genetic regulators of apical constriction and gain mechanistic insight into the cell biology of this process, we need reliable assay systems that allow real-time observation and quantification of apical constriction as it occurs and permit gain- and loss-of-function analyses to explore gene function and interaction during apical constriction. In this chapter, we describe using the early Xenopus embryo as an assay system to investigate molecular mechanisms involved in apical constriction during both gastrulation and neurulation.

Comparative Effects of Methanol and Aqueous Extracts of Corchorus olitorius Plant on Haematology and Some Reproductive Indices of Male Wistar Rats

Corchorus olitorius is a vegetable plant/shrub and the leaves are very nutritious and rich in vitamins, minerals and dietary fibers. The study was carried out to identify the effects two extracts of this plant on the reproductive indices of male Wistar rats Forty-five adult male rats of about 12 weeks old, each weighing about 120g were used for this study, kept in a cage and fed with commercial rat pellets and water was given at ad-libitum. They were randomly divided into groups A, B and C of 15 rats per group. 250mg/kg of the leaf extract was administered orogastrically using once daily for 21 days. Group A and B were treated with methanol and aqueous leaves of Corchorus extract respectively and Group C was given distilled water and served as the control. The weekly sacrifice of five rats per group was done following treatments. In this study, it was observed at the first-week post -treatment that there was significant (p≤0.05) decrease in the PCV and haemoglobin values of group A rats compared to the control group but the values later increased at the second week and third-week post-treatments. There was also a significant decrease in spermatozoa motility in the treated groups A and B compared to the control group C at the first, second- and third-week post treatments. Also, with the results of the serum testosterone level of group A and B compared to group C. The value was higher in group A followed by group B whereas, at the second week and third week, there was no significant difference in the values of the serum testosterone levels compared to the control groups. It is therefore concluded that the methanol and aqueous extract of Corchorus olitorius leaves significantly decreased sperm motility in male albino rats hence could decrease male fertility.

Xenopus as a platform for discovery of genes relevant to human disease

Congenital birth defects result from an abnormal development of an embryo and have detrimental effects on children's health. Specifically, congenital heart malformations are a leading cause of death among pediatric patients and often require surgical interventions within the first year of life. Increased efforts to navigate the human genome provide an opportunity to discover multiple candidate genes in patients suffering from birth defects. These efforts, however, fail to provide an explanation regarding the mechanisms of disease pathogenesis and emphasize the need for an efficient platform to screen candidate genes. Xenopus is a rapid, cost effective, high-throughput vertebrate organism to model the mechanisms behind human disease. This review provides numerous examples describing the successful use of Xenopus to investigate the contribution of patient mutations to complex phenotypes including congenital heart disease and heterotaxy. Moreover, we describe a variety of unique methods that allow us to rapidly recapitulate patients' phenotypes in frogs: gene knockout and knockdown strategies, the use of fate maps for targeted manipulations, and novel imaging modalities. The combination of patient genomics data and the functional studies in Xenopus will provide necessary answers to the patients suffering from birth defects. Furthermore, it will allow for the development of better diagnostic methods to ensure early detection and intervention. Finally, with better understanding of disease pathogenesis, new treatment methods can be tailored specifically to address patient's phenotype and genotype.

Immunofluorescence of Microtubule Assemblies in Amphibian Oocytes and Early Embryos

Amphibian oocytes and embryos are classical models to study cellular and developmental processes. For these studies, it is often advantageous to visualize protein organization. However, the large size and yolk distribution make imaging of deep structures in amphibian zygotes challenging. Here we describe in detail immunofluorescence (IF) protocols for imaging microtubule assemblies in early amphibian development. We developed these protocols to elucidate how the cell division machinery adapts to drastic changes in embryonic cell sizes. We describe how to image mitotic spindles, microtubule asters, chromosomes, and nuclei in whole-mount embryos, even when they are hundreds of micrometers removed from the embryo's surface. Though the described methods were optimized for microtubule assemblies, they have also proven useful for the visualization of other proteins.

Protein localization screening in vivo reveals novel regulators of multiciliated cell development and function

Multiciliated cells (MCCs) drive fluid flow in diverse tubular organs and are essential for the development and homeostasis of the vertebrate central nervous system, airway and reproductive tracts. These cells are characterized by dozens or hundreds of motile cilia that beat in a coordinated and polarized manner. In recent years, genomic studies have not only elucidated the transcriptional hierarchy for MCC specification but also identified myriad new proteins that govern MCC ciliogenesis, cilia beating and cilia polarization. Interestingly, this burst of genomic data has also highlighted that proteins with no obvious role in cilia do, in fact, have important ciliary functions. Understanding the function of proteins with little prior history of study presents a special challenge, especially when faced with large numbers of such proteins. Here, we define the subcellular localization in MCCs of ∼200 proteins not previously implicated in cilia biology. Functional analyses arising from the screen provide novel links between actin cytoskeleton and MCC ciliogenesis.

Animal models of smoke inhalation injury and related acute and chronic lung diseases

Smoke inhalation injury leads to various acute and chronic lung diseases and thus is the dominant cause of fire-related fatalities. In a search for an effective treatment and validation of therapies different classes of animal models have been developed, which include both small and large animals. These models have advanced our understanding of the mechanism of smoke inhalation injury, enabling a better understanding of pathogenesis and pathophysiology and development of new therapies. However, none of the animal models fully mirrors human lungs and their pathologies. All animal models have their limitations in replicating complex clinical conditions associated with smoke inhalation injury in humans. Therefore, for a correct interpretation of the results and to avoid bias, a precise understanding of similarities and differences of lungs between different animal species and humans is critical. We have reviewed and presented comprehensive comparison of different animal models and their clinical relevance. We presented an overview of methods utilized to induce smoke inhalation injuries, airway micro-/macrostructure, advantages and disadvantages of the most commonly used small and large animal models.

An angiogenesis platform using a cubic artificial eggshell with patterned blood vessels on chicken chorioallantoic membrane

The chorioallantoic membrane (CAM) containing tiny blood vessels is an alternative to large animals for studies involving angiogenesis and tissue engineering. However, there is no technique to design the direction of growing blood vessels on the CAM at the microscale level for tissue engineering experiments. Here, a methodology is provided to direct blood vessel formation on the surface of a three-dimensional egg yolk using a cubic artificial eggshell with six functionalized membranes. A structure on the lateral side of the eggshell containing a straight channel and an interlinked chamber was designed, and the direction and formation area of blood vessels with blood flow was artfully defined by channels with widths of 70-2000 μm, without sharply reducing embryo viability. The relationship between the size of interlinked chamber and the induction of blood vessels was investigated to establish a theory of design. Role of negative and positive pressure in the induction of CAM with blood vessels was investigated, and air pressure change in the culture chamber was measured to demonstrate the mechanism for blood vessel induction. Histological evaluation showed that components of CAM including chorionic membrane and blood vessels were induced into the channels. Based on our design theory, blood vessels were induced into arrayed channels, and channel-specific injection and screening were realized, which demonstrated proposed applications. The platform with position- and space-controlled blood vessels is therefore a powerful tool for biomedical research, which may afford exciting applications in studies involved in local stimulation of blood vessel networks and those necessary to establish a living system with blood flow from a beating heart.

Developmental changes in head movement kinematics during swimming in Xenopus laevis tadpoles

During the post-embryonic developmental growth of animals, a number of physiological parameters such as locomotor performance, dynamics and behavioural repertoire are adjusted to match the requirements determined by changes in body size, proportions and shape. Moreover, changes in movement parameters also cause changes in the dynamics of self-generated sensory stimuli, to which motion-detecting sensory systems have to adapt. Here, we examined head movements and swimming kinematics of Xenopus laevis tadpoles with a body length of 10-45 mm (developmental stage 46-54) and compared these parameters with fictive swimming, recorded as ventral root activity in semi-intact in vitro preparations. Head movement kinematics was extracted from high-speed video recordings of freely swimming tadpoles. Analysis of these locomotor episodes indicated that the swimming frequency decreased with development, along with the angular velocity and acceleration of the head, which represent self-generated vestibular stimuli. In contrast, neither head oscillation amplitude nor forward velocity changed with development despite the ∼3-fold increase in body size. The comparison between free and fictive locomotor dynamics revealed very similar swimming frequencies for similarly sized animals, including a comparable developmental decrease of the swimming frequency. Body morphology and the motor output rhythm of the spinal central pattern generator therefore develop concurrently. This study thus describes development-specific naturalistic head motion profiles, which form the basis for more natural stimuli in future studies probing the vestibular system.

Color and intensity discrimination in Xenopus laevis tadpoles

Investigations into the physiology of Xenopus laevis have the potential to greatly accelerate biomedical research, especially concerning neural plasticity and sensory systems, but are limited by the lack of available information on behavioral learning in this species. Here, we attempt to lay the foundations for a behavioral assay in Xenopus that can be used in conjunction with biological manipulations. We tested cohorts of Xenopus tadpoles across four light-mediated active-avoidance experiments, using either wavelength or intensity as the salient discriminative cue. In the wavelength task, we determine a baseline learning rate and characterize retention of learning, identifying active extinction effects as far more potent than the passage of time in the loss of behavior. In the intensity task, we examine the effects of varying differences between the discriminative stimuli on acquisition and extinction and identify a critical range of intensity differences where learning changes. The results of our experiments demonstrate that Xenopus is a tractable model organism for cognitive research and can learn a variety of associative tasks in the laboratory settings. These data reveal new aspects of the Xenopus larval visual processing system and facilitate future research between cognitive methods and biological/chemical manipulations to study mechanisms of brain structure and function.

Quantifying Demyelination in NK venom treated nerve using its electric circuit model

Reduction of myelin in peripheral nerve causes critical demyelinating diseases such as chronic inflammatory demyelinating polyneuropathy, Guillain-Barre syndrome, etc. Clinical monitoring of these diseases requires rapid and non-invasive quantification of demyelination. Here we have developed formulation of nerve conduction velocity (NCV) in terms of demyelination considering electric circuit model of a nerve having bundle of axons for its quantification from NCV measurements. This approach has been validated and demonstrated with toad nerve model treated with crude Naja kaouthia (NK) venom and also shows the effect of Phospholipase A2 and three finger neurotoxin from NK-venom on peripheral nerve. This opens future scope for non-invasive clinical measurement of demyelination.

Xenopus as a model organism for birth defects-Congenital heart disease and heterotaxy

Congenital heart disease is the leading cause of birth defects, affecting 9 out of 1000 newborns each year. A particularly severe form of congenital heart disease is heterotaxy, a disorder of left-right development. Despite aggressive surgical management, patients with heterotaxy have poor survival rates and severe morbidity due to their complex congenital heart disease. Recent genetic analysis of affected patients has found novel candidate genes for heterotaxy although their underlying mechanisms remain unknown. In this review, we discuss the importance and challenges of birth defects research including high locus heterogeneity and few second alleles that make defining disease causality difficult. A powerful strategy moving forward is to analyze these candidate genes in a high-throughput human disease model. Xenopus is ideal for these studies. We present multiple examples demonstrating the power of Xenopus in discovering new biology from the analysis of candidate heterotaxy genes such as GALNT11, NEK2 and BCOR. These genes have diverse roles in embryos and have led to a greater understanding of complex signaling pathways and basic developmental biology. It is our hope that the mechanistic analysis of these candidate genes in Xenopus enabled by next generation sequencing of patients will provide clinicians with a greater understanding of patient pathophysiology allowing more precise and personalized medicine, to help patients more effectively in the future.

Egg-in-cube: design and fabrication of a novel artificial eggshell with functionalized surface

An eggshell is a porous microstructure that regulates the passage of gases to allow respiration. The chick embryo and its circulatory system enclosed by the eggshell has become an important model for biomedical research such as the control of angiogenesis, cancer therapy, and drug delivery test, because the use of embryo is ethically acceptable and it is inexpensive and small. However, chick embryo and extra-embryonic blood vessels cannot be accessed freely and has poor observability because the eggshell is tough and cannot be seen through, which limits its application. In this study, a novel artificial eggshell with functionalized surface is proposed, which allows the total amount of oxygen to pass into the egg for the chick embryo culturing and has high observability and accessibility for embryo manipulation. First, a 40-mm enclosed cubic-shaped eggshell consisting of a membrane structure and a rigid frame structure is designed, and then the threshold of the membrane thickness suitable for the embryo survival is figured out according to the oxygen-permeability of the membrane structure. The designed artificial eggshell was actually fabricated by using polydimethylsiloxane (PDMS) and polycarbonate (PC) in the current study. Using the fabricated eggshell, chick embryo and extra-embryonic blood vessels can be observed from multiple directions. To test the effectiveness of the design, the cubic eggshells were used to culture chick embryos and survivability was confirmed when PDMS membranes with adequate oxygen permeability were used. Since the surface of the eggshell is transparent, chick embryo tissue development could be observed during the culture period. Additionally, the chick embryo tissues could be accessed and manipulated from outside the cubic eggshell, by using mechanical tools without breakage of the eggshell. The proposed "Egg-in-Cube" with functionalized surface has great potential to serve as a promising platform for biomedical research.

Breeding based remobilization of Tol2 transposon in Xenopus tropicalis

Xenopus is a powerful model for studying a diverse array of biological processes. However, despite multiple methods for transgenesis, relatively few transgenic reporter lines are available and commonly used. Previous work has demonstrated that transposon based strategies are effective for generating transgenic lines in both invertebrate and vertebrate systems. Here we show that the Tol2 transposon can be remobilized in the genome of X. tropicalis and passed through the germline via a simple breeding strategy of crossing transposase expressing and transposon lines. This remobilization system provides another tool to exploit transgenesis and opens new opportunities for gene trap and enhancer trap strategies.

Manipulating and imaging the early Xenopus laevis embryo

Over the past half century, the Xenopus laevis embryo has become a popular model system for studying vertebrate early development at molecular, cellular, and multicellular levels. The year-round availability of easily fertilized eggs, the embryo's large size and rapid development, and the hardiness of both adults and offspring against a wide range of laboratory conditions provide unmatched advantages for a variety of approaches, particularly "cutting and pasting" experiments, to explore embryogenesis. There is, however, a common perception that the Xenopus embryo is intractable for microscope work, due to its store of large, refractile yolk platelets and abundant cortical pigmentation. This chapter presents easily adapted protocols to surmount, and in some cases take advantage of, these optical properties to facilitate live-cell microscopic analysis of commonly used experimental manipulations of early Xenopus embryos.