Xenopus as a model system for vertebrate heart development

The African clawed frog, Xenopus laevis, is a valuable model system for studies of vertebrate heart development. In the following review, we describe a range of embryological and molecular methodologies that are used in Xenopus research and discuss key discoveries relating to heart development that have been made using this model system. We also discuss how the sequence of the Xenopus tropicalis genome provides a valuable tool for identification of orthologous genes and for identification of evolutionarily conserved promoter elements. Finally, both forward and reverse genetic approaches are currently being applied to Xenopus for the study of vertebrate heart development.     

Tracheal development in Drosophila melanogaster as a model system for studying the development of a branched organ

The development of the tracheal system of Drosophila melanogaster represents a paradigm for studying the molecular mechanisms involved in the formation of a branched tubular network. Tracheogenesis has been characterized at the morphological, cellular and genetic level and a series of successive, but linked events have been described as the basis for the formation of the complex network of tubules which extend over the entire organism. Tracheal cells stop to divide early in the process of tracheogenesis and the formation of the interconnected network requires highly controlled cell migration events and cell shape changes. A number of genes involved in these two processes have been identified but in order to obtain a more complete view of branching morphogenesis, many more genes carrying essential functions have to be isolated and characterized. Here, we provide a progress report on our attempts to identify further genes expressed in the tracheal system. We show that empty spiracles (ems), a head gap gene, is required for the formation of a specific tracheal branch, the visceral branch. We also identified a Sulfotransferase and a Multiple Inositol Polyphosphate phosphatase that are strongly upregulated in tracheal cells and discuss their possible involvement in tracheal development.     

Yeast as a model system for understanding the control of DNA replication in eukaryotes

In the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, the initiation of DNA replication is controlled at a point called START. At this point, the cellular environment is assessed; only if conditions are appropriate do cells traverse START, thus becoming committed to initiate DNA replication and complete the remainder of the cell cycle. The cdc2⁺ / CDC28⁺ gene, encoding the protein kinase p34, is a key element in this complex control. The identification of structural and functional homologues of p34 suggests that it has a role in the control of DNA replication in all eukaryotes. The WHI1⁺, CLN1⁺ and CLN2⁺ gene products, identified in S. cerevisiae, are positive regulators that function at START and may interact with p34. Determining how passing the START control point leads to the initiation of DNA replication is a major outstanding challenge in cell cycle studies.     

The rice field eel as a model system for vertebrate sexual development

Complex developmental mechanisms of vertebrates are unraveled using comparative genomic approaches. Several teleosts, such as zebrafish, medaka and pufferfish, are used as genetic model systems because they are amenable to studies of gene function. The rice field eel, a freshwater fish, is emerging as a specific model system for studies of vertebrate sexual development because of its small genome size and naturally occurring sex reversal. Data presented here support the use of the rice field eel as another important fish model for comparative genome studies, especially in vertebrate sexual development. This model system is complementary rather than redundant.     

Drosophila melanogaster as a model system for assessing development under conditions of microgravity

More is known about the regulation of early developmental events in Drosophila than any other animal. In addition, its size and short life cycle make it a facile experimental system. Since developmental perturbations have been demonstrated when both oogenesis and embryogenesis occur in the space environment, there is a strong rationale for using this organism for the elucidation of specific gravity-sensitive developmental events.     

Stability of the human respiratory control system I. Analysis of a two-dimensional delay state-space model

A number of mathematical models of the human respiratory control system have been developed since 1940 to study a wide range of features of this complex system. Among them, periodic breathing (including Cheyne-Stokes respiration and apneustic breathing) is a collection of regular but involuntary breathing patterns that have important medical implications. The hypothesis that periodic breathing is the result of delay in the feedback signals to the respiratory control system has been studied since the work of Grodins et al. in the early 1950's [12]. The purpose of this paper is to study the stability characteristics of a feedback control system of five differential equations with delays in both the state and control variables presented by Khoo et al. [17] in 1991 for modeling human respiration. The paper is divided in two parts. Part I studies a simplified mathematical model of two nonlinear state equations modeling arterial partial pressures of O2 and CO2 and a peripheral controller. Analysis was done on this model to illuminate the effect of delay on the stability. It shows that delay dependent stability is affected by the controller gain, compartmental volumes and the manner in which changes in the ventilation rate is produced (i.e., by deeper breathing or faster breathing). In addition, numerical simulations were performed to validate analytical results. Part II extends the model in Part I to include both peripheral and central controllers. This, however, necessitates the introduction of a third state equation modeling CO2 levels in the brain. In addition to analytical studies on delay dependent stability, it shows that the decreased cardiac output (and hence increased delay) resulting from the congestive heart condition can induce instability at certain control gain levels. These analytical results were also confirmed by numerical simulations.     

Stability of the human respiratory control system II. Analysis of a three-dimensional delay state-space model

A number of mathematical models of the human respiratory control system have been developed since 1940 to study a wide range of features of this complex system. Among them, periodic breathing (including Cheyne-Stokes respiration and apneustic breathing) is a collection of regular but involuntary breathing patterns that have important medical implications. The hypothesis that periodic breathing is the result of delay in the feedback signals to the respiratory control system has been studied since the work of Grodins et al. in the early 1950's [1]. The purpose of this paper is to study the stability characteristics of a feedback control system of five differential equations with delays in both the state and control variables presented by Khoo et al. [4] in 1991 for modeling human respiration. The paper is divided in two parts. Part I studies a simplified mathematical model of two nonlinear state equations modeling arterial partial pressures of O2 and CO2 and a peripheral controller. Analysis was done on this model to illuminate the effect of delay on the stability. It shows that delay dependent stability is affected by the controller gain, compartmental volumes and the manner in which changes in the ventilation rate is produced (i.e., by deeper breathing or faster breathing). In addition, numerical simulations were performed to validate analytical results. Part II extends the model in Part I to include both peripheral and central controllers. This, however, necessitates the introduction of a third state equation modeling CO2 levels in the brain. In addition to analytical studies on delay dependent stability, it shows that the decreased cardiac output (and hence increased delay) resulting from the congestive heart condition can induce instability at certain control gain levels. These analytical results were also confirmed by numerical simulations.     

Function of alveoli as a result of evolutionary development of respiratory system in mammals

Reaction of hemoglobin oxygenation is known to occur for 40 femtoseconds (40 × 10^?15 s). However, the process of oxygen diffusion to hemoglobin under physiologic conditions decelerated this reaction approximately billion times. In mammalian lungs, blood is moving at a high rate and in a relatively high amount. The human lung mass is as low as 600 g, but the complete cardiac output approaches 6 l/min. In rat, from 20 to 40 ml of blood is passed for one minute through the lung whose mass is about 1.5 g. Such blood flow rate is possible, as in lungs of high animals there exists a dense network of relatively large microvessels with diameter from 20 to 40 μm and more. In spite of a large volume and a high blood flow rate hampering oxygen diffusion, the complete blood oxygenation occurs in lung alveoli. This is due to peculiar mechanisms that facilitate markedly the oxygen diffusion and that developed in alveoli of mammals in the course of many million years of evolution of their respiratory system. Thus, alveolus is not a bubble with air, but a complex tool of fight with inertness of diffusion. It is interesting that in lungs of the low vertebrates, neither such system of blood vessels nor alveoli exist, and their blood flow rate is much lower than in mammals.     

The fictively breathing tadpole brainstem preparation as a model for the development of respiratory pattern generation and central chemoreception

Spontaneous high-frequency, low-amplitude and low-frequency, high-amplitude efferent bursting patterns of cranial and spinal motor nerve activity in the in vitro brainstem preparation of the bullfrog tadpole Rana catesbeiana have been characterized as fictive gill and lung ventilation, respectively (Gdovin MJ, Torgerson CS, Remmers JE). Characterization of gill and lung ventilatory activity in cranial nerves in the spontaneously breathing tadpole Rana catesbeiana, FASEB J 1996;10(3):A642; Gdovin MJ, Torgerson CS, Remmers JE. Neurorespiratory pattern of gill and lung ventilation in the decerebrate spontaneously breathing tadpole, Respir Physiol 1998;113:135 146; Pack AI, Galante RJ, Walker RE, Kubin LK, Fishman AP. Comparative approach to neural control of respiration, In: Speck DF, Dekin MS, Revelette WR, Frazier DT, editors. Respiratory Control Central and Peripheral Mechanisms. Lexington: University of Kentucky Press, 1993:52-57). In addition, the ontogenetic dependence of central respiratory chemoreceptor stimulation on fictive gill and lung ventilation has been previously described (Torgerson CS, Gdovin MJ, Remmers JE. Fictive gill and lung ventilation in the pre- and post-metamorphic tadpole brainstem, J Neurophysiol 1998, in press). To investigate the neural substrates responsible for central respiratory rhythm generation of gill and lung ventilation in the developing tadpole, we recorded efferent activities of cranial nerve (CN) V, VII, and X and spinal nerve (SN) II during changes in superfusate PCO2 before and after multiple transection of the in vitro brainstem. The brainstem was transected between CN VIII and IX and the response to changes in PCO2 was recorded. A second transection was then made between the caudal margin of CN X and rostral to SN II. Preliminary data reveal that robust gill ventilation was recorded consistently only if the segment of brainstem included CN X, whereas the loci capable of eliciting fictive lung bursting patterns appeared to differ depending on developmental stage. These data demonstrate that the neural substrate required for fictive gill and lung ventilation exists in anatomically separate regions such that the gill central pattern generator (CPG) is located in the caudal medulla at the level of CN X throughout development, whereas the location of the lung CPG is located more rostrally at the level of CN VII in the post-metamorphic larva. Both in vivo and in vitro studies revealed two distinct neural bursting patterns associated with gill and lung ventilation. Sequential activation of CN V, VII, X were observed during gill ventilation of in vivo and fictive gill ventilation in vitro, whereas these nerve activities, along with SN II displayed more synchronous bursting patterns of activation during lung ventilation and fictive lung breaths.     

Japanese quail as a model system for studying the neuroendocrine control of reproductive and social behaviors

Japanese quail (Coturnix japonica; referred to simply as quail in this article) readily exhibit sexual behavior and related social behaviors in captive conditions and have therefore proven valuable for studies of how early social experience can shape adult mate preference and sexual behavior. Quail have also been used in sexual conditioning studies illustrating that natural stimuli predict successful reproduction via Pavlovian processes. In addition, they have proven to be a good model to study how variation in photoperiod regulates reproduction and how variation in gonadal steroid hormones controls sexual behavior. For example, studies have shown that testosterone activates male-typical behaviors after being metabolized into estrogenic and androgenic metabolites. A critical site of action for these metabolites is the medial preoptic nucleus (POM), which is larger in males than in females. The enzyme aromatase converts testosterone to estradiol and is enriched in the POM in a male-biased fashion. Quail studies were the first to show that this enzyme is regulated both relatively slowly via genomic actions of steroids and more quickly via phosphorylation. With this base of knowledge and the recent cloning of the entire genome of the closely related chicken, quail will be valuable for future studies connecting gene expression to sexual and social behaviors.     

Adaptation in the respiratory control system

Exposure to hypoxia, whether for short or prolonged periods or for repeated episodes, produces alterations in the ventilatory responses. This review presents evidence that these adaptations are likely to be mediated by adaptations in the respiratory chemoreflexes, particularly the peripheral chemoreflex, and proposes models of respiratory control explaining the observed changes in ventilation. After a brief introduction to the respiratory control system, a graphical model is developed that illustrates the operation of the system in the steady state, which will be used later. Next, the adaptations in ventilatory responses to hypoxia that have been observed are described, and methods of measuring the alterations in the chemoreflexes that might account for them are discussed. Finally, experimental data supporting the view that changes in the activity of the peripheral chemoreflex can account for the ventilatory adaptations to hypoxia are presented and incorporated into models of chemoreflex behaviour during exposures to hypoxia of various durations.     

Amphibians as models for studying environmental change

The use of amphibians as models in ecological research has a rich history. From an early foundation in studies of amphibian natural history sprang generations of scientists who used amphibians as models to address fundamental questions in population and community ecology. More recently, in the wake of an environment that human disturbances rapidly altered, ecologists have adopted amphibians as models for studying applied ecological issues such as habitat loss, pollution, disease, and global climate change. Some of the characteristics of amphibians that make them useful models for studying these environmental problems are highlighted, including their trophic importance, environmental sensitivity, research tractability, and impending extinction. The article provides specific examples from the recent literature to illustrate how studies on amphibians have been instrumental in guiding scientific thought on a broad scale. Included are examples of how amphibian research has transformed scientific disciplines, generated new theories about global health, called into question widely accepted scientific paradigms, and raised awareness in the general public that our daily actions may have widespread repercussions. In addition, studies on amphibian declines have provided insight into the complexity in which multiple independent factors may interact with one another to produce catastrophic and sometimes unpredictable effects. Because of the complexity of these problems, amphibian ecologists have been among the strongest advocates for interdisciplinary research. Future studies of amphibians will be important not only for their conservation but also for the conservation of other species, critical habitats, and entire ecosystems.     

Antibodies as a model system for comparative model refinement

Predicting the conformations of loops is a critical aspect of protein comparative (homology) modeling. Despite considerable advances in developing loop prediction algorithms, refining loops in homology models remains challenging. In this work, we use antibodies as a model system to investigate strategies for more robustly predicting loop conformations when the protein model contains errors in the conformations of side chains and protein backbone surrounding the loop in question. Specifically, our test system consists of partial models of antibodies in which the “scaffold” (i.e., the portion other than the complementarity determining region, CDR, loops) retains native backbone conformation, whereas the CDR loops are predicted using a combination of knowledge‐based modeling (H1, H2, L1, L2, and L3) and ab initio loop prediction (H3). H3 is the most variable of the CDRs. Using a previously published method, a test set of 10 shorter H3 loops (5–7 residues) are predicted to an average backbone (N? Cα? C? O) RMSD of 2.7 Å while 11 longer loops (8–9 residues) are predicted to 5.1 Å, thus recapitulating the difficulties in refining loops in models. By contrast, in control calculations predicting the same loops in crystal structures, the same method reconstructs the loops to an average of 0.5 and 1.4 Å for the shorter and longer loops, respectively. We modify the loop prediction method to improve the ability to sample near‐native loop conformations in the models, primarily by reducing the sensitivity of the sampling to the loop surroundings, and allowing the other CDR loops to optimize with the H3 loop. The new method improves the average accuracy significantly to 1.3 Å RMSD and 3.1 Å RMSD for the shorter and longer loops, respectively. Finally, we present results predicting 8–10 residue loops within complete comparative models of five nonantibody proteins. While anecdotal, these mixed, full‐model results suggest our approach is a promising step toward more accurately predicting loops in homology models. Furthermore, while significant challenges remain, our method is a potentially useful tool for predicting antibody structures based on a known Fv scaffold. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Yeast as a model of human mitochondrial tRNA base substitutions: investigation of the molecular basis of respiratory defects

We investigate the relationships between acylation defects and structure alterations due to base substitutions in yeast mitochondrial (mt) tRNA(UUR)(Leu). The studied substitutions are equivalent to the A3243G and T3250C human pathogenetic tRNA mutations. Our data show that both mutations can produce tRNA(UUR)(Leu) acylation defects, although to a different extent. For mutant A14G (equivalent to MELAS A3243G base substitution), the presence of the tRNA and its defective aminoacylation could be observed only in the nuclear context of W303, a strain where the protein synthesis defects caused by tRNA base substitutions are far less severe than in previously studied strains. For mutant T20C (equivalent to the MM/CPEO human T3250C mutation), the acylation defect was less severe, and a thermosensitive acylation could be detected also in the MCC123 strain. The correlation between the severity of the in vivo phenotypes of yeast tRNA mutants and those obtained in in vitro studies of human tRNA mutants supports the view that yeast is a suitable model to study the cellular and molecular effects of tRNA mutations involved in human pathologies. Furthermore, the yeast model offers the possibility of modulating the severity of yeast respiratory phenotypes by studying the tRNA mutants in different nuclear contexts. The nucleotides at positions 14 and 20 are both highly conserved in yeast and human mt tRNAs; however, the different effect of their mutations can be explained by structure analyses and quantum mechanics calculations that can shed light on the molecular mechanisms responsible for the experimentally determined defects of the mutants.     

Amphibians as research models for regenerative medicine

The ability to regenerate bone across a critical size defect would be a marked clinical advance over current methods for dealing with such structural gaps. Here, we briefly review the development of limb bones and the mandible, the regeneration of urodele limbs after amputation, and present evidence that urodele and anuran amphibians represent a valuable research model for the study of segment defect regeneration in both limb bones and mandible.     

The chicken as a model for embryonic development

The traditional strength of chicken embryos for studying development is that they are readily manipulated. This has led to some major discoveries in developmental biology such as the demonstration that the neural crest gives rise to almost the entire peripheral nervous system and the identification of signalling centres that specify the pattern of structures in the central nervous system and limb. More recently with the burgeoning discovery of developmentally important genes, chicken embryos have provided useful models for testing function. Uncovering the molecular basis of development provides direct links with clinical genetics. In addition, since many genes that have crucial roles in development are also expressed in tumours, basic research on chickens has implications for understanding human health and disease. Now that the chicken genome has been sequenced and genomic resources for chicken are becoming increasingly available, this opens up opportunities for combining these new technologies with the manipulability of chicken embryos and also exploiting comparative genomics.     

Ciona intestinalis as a model for cardiac development

The primitive chordate Ciona intestinalis has emerged as a significant model system for the study of heart development. The Ciona embryo employs a conserved heart gene network in the context of extremely low cell numbers and reduced genetic redundancy. Here, I review recent studies on the molecular genetics of Ciona cardiogenesis as well as classic work on heart anatomy and physiology. I also discuss the potential of employing Ciona to decipher a comprehensive chordate gene network and to determine how this network controls heart morphogenesis.