Xiphophorus interspecies hybrids as genetic models of induced neoplasia

Phylogenomics analyses of all species of Swordtails (Genus Xiphophorus ) highlights hybridization precedes speciation

Hybridization has been recognized as an important driving force for evolution, however studies of the genetic consequence and its cause are still lagging behind in vertebrates due to the lack of appropriate experimental systems. Fish of the central American genus Xiphophorus were proposed to have evolved with multiple ancient and ongoing hybridization events, and served as a valuable research model in evolutionary biology and in biomedical research on human disease for more than a century. Here, we provide the complete genome resource and its annotation of all 26 Xiphophorus species. On this dataset we resolved the so far conflicting phylogeny. Through comparative genomic analyses we investigated the molecular evolution of genes related to melanoma, for a main sexually selected trait and for the genetic control of puberty timing, which are predicted to be involved in pre-and postzygotic isolation and thus to influence the probability of interspecific hybridization in Xiphophorus . We demonstrate dramatic size-variation of some gene families across species, despite the reticulate evolution and short divergence time. Finally, we clarify the hybridization history in the genus Xiphophorus genus, settle the long dispute on the hybridization origin of two Southern swordtails, highlight hybridizations precedes speciation, and reveal the distribution of hybridization ancestry remaining in the fused genome.

Validity of Xiphophorus fish as models for human disease

Platyfish and swordtails of the genus Xiphophorus provide a well-established model for melanoma research and have become well known for this feature. Recently, modelling approaches for other human diseases in Xiphophorus have been developed or are emerging. This Review provides a comprehensive summary of these models and discusses how findings from basic biological and molecular studies and their translation to medical research demonstrate that Xiphophorus models have face, construct and predictive validity for studying a broad array of human diseases. These models can thus improve our understanding of disease mechanisms to benefit patients.

Platyfish bypass the constraint of the caudal fin ventral identity in teleosts

BACKGROUND

The caudal fin of teleosts is characterized by dorsoventral symmetry. Despite this external morphology, the principal rays of this appendage connect to bones below the notochord, indicating the ventral (hypochordal) identity of this organ.

RESULTS

Here, we report that this typical architecture of the caudal fin is not fully conserved in the platyfish (Xiphophorus maculatus) and the guppy (Poecilia reticulata), representatives of the Poeciliidae family. We show that in these species, 3-4 principal rays connect to bones above the notochord, suggesting an epichordal contribution. Consistently, as examined in platyfish, dorsal identity genes zic1/4 were highly expressed in these rays, providing molecular evidence of their epichordal origin. Developmental analysis revealed that the earliest rays above the notochord emerge at the 10-ray stage of fin morphogenesis. In contrast to zebrafish and medaka, platyfish and guppies display a mirrored shape of dorsal and ventral processes of the caudal endoskeleton. Our study suggests that an ancestral bauplan expanded in poeciliids by advancing its symmetrical pattern.

CONCLUSION

The platyfish evolved a fin architecture with the epichordal origin of its upper principal rays and a high level of symmetry in the caudal endoskeleton. This innovative architecture highlights the adaptation of the teleost skeleton.

An Open-Hardware Insemination Device for Small-Bodied Live-Bearing Fishes to Support Development and Use of Germplasm Repositories

Small-bodied live-bearing fishes attract broad attention because of their importance in biomedical research and critical conservation status in natural habitats. Artificial insemination is an essential process to establish hybrid lines and for the operation of sperm repositories. The existing mouth-pipetting technique for artificial insemination of live-bearing fishes has not been substantially upgraded since the first implementation in the 1950s. The goal of this work was to develop a standardized artificial inseminator device (SAID) to address issues routinely encountered in insemination by mouth-pipetting, including lack of reproducibility among different users, difficulty in training, and large unreportable variation in sample volume and pressure during insemination. Prototypes of the SAID were designed as relatively inexpensive (<USD 80) open hardware based on commercially available and 3-D printed components to enable broad community access. A linear actuator was used to accurately control the position of a piston for fluid transfer with a standard deviation of <0.1 mm over a 4 mm range of travel. The volume of sample transfer was precisely controlled with a linear relationship (r2 > 0.99) between the piston position and volume. Pressure generation from eight mouth-pipetting operators and SAID prototypes were assessed by pressure sensors. The pressure control by SAID was superior to that produced by mouth-pipetting, yielding lower pressures (31−483 Pa) and smaller variations (standard deviation <11 Pa). These pressures were sufficient to deliver 1−5 μL of fluid into female reproductive tracts yet low enough to avoid physical injury to fish. Community-level enhancements of the SAID prototype could enable standardized insemination with minimal training and facilitate the participation of research communities in the use of cryopreserved genetic resources.

Nanotechnology Addressing Cutaneous Melanoma: The Italian Landscape

Cutaneous melanoma is one of the most aggressive solid tumors, with a low survival for the metastatic stage. Currently, clinical melanoma treatments include surgery, chemotherapy, targeted therapy, immunotherapy and radiotherapy. Of note, innovative therapeutic regimens concern the administration of multitarget drugs in tandem, in order to improve therapeutic efficacy. However, also, if this drug combination is clinically relevant, the patient's response is not yet optimal. In this scenario, nanotechnology-based delivery systems can play a crucial role in the clinical treatment of advanced melanoma. In fact, their nano-features enable targeted drug delivery at a cellular level by overcoming biological barriers. Various nanomedicines have been proposed for the treatment of cutaneous melanoma, and a relevant number of them are undergoing clinical trials. In Italy, researchers are focusing on the pharmaceutical development of nanoformulations for malignant melanoma therapy. The present review reports an overview of the main melanoma-addressed nanomedicines currently under study in Italy, alongside the state of the art of melanoma therapy. Moreover, the latest Italian advances concerning the pre-clinical evaluation of nanomedicines for melanoma are described.

Oncogenic allelic interaction in Xiphophorus highlights hybrid incompatibility

The Bateson–Dobzhansky–Muller (BDM) model describes negative epistatic interactions that occur between genes with a different evolutionary history to account for hybrid incompatibility and is a central theory explaining genetic mechanisms underlying speciation. Since the early 1900 s when the BDM model was forwarded examples of BDM incompatibility have been described in only a few nonvertebrate cases. This study reports the only vertebrate system, with clearly defined interacting loci, that supports the BDM model. In addition, this study also poses that tumorigenesis serves as a novel mechanism that accounts for postzygotic isolation.

Mixing genomes of different species by hybridization can disrupt species-specific genetic interactions that were adapted and fixed within each species population. Such disruption can predispose the hybrids to abnormalities and disease that decrease the overall fitness of the hybrids and is therefore named as hybrid incompatibility. Interspecies hybridization between southern platyfish and green swordtails leads to lethal melanocyte tumorigenesis. This occurs in hybrids with tumor incidence following progeny ratio that is consistent with two-locus interaction, suggesting melanoma development is a result of negative epistasis. Such observations make Xiphophorus one of the only two vertebrate hybrid incompatibility examples in which interacting genes have been identified. One of the two interacting loci has been characterized as a mutant epidermal growth factor receptor. However, the other locus has not been identified despite over five decades of active research. Here we report the localization of the melanoma regulatory locus to a single gene, rab3d, which shows all expected features of the long-sought oncogene interacting locus. Our findings provide insights into the role of egfr regulation in regard to cancer etiology. Finally, they provide a molecular explainable example of hybrid incompatibility.

Intra-Strain Genetic Variation of Platyfish (Xiphophorus maculatus) Strains Determines Tumorigenic Trajectory

Xiphophorus interspecies hybrids represent a valuable model system to study heritable tumorigenesis, and the only model system that exhibits both spontaneous and inducible tumors. Types of tumorigenesis depend on the specific pedigree of the parental species, X. maculatus, utilized to produce interspecies hybrids. Although the ancestors of the two currently used X. maculatus parental lines, Jp163 A and Jp163 B, were originally siblings produced by the same mother, backcross interspecies hybrid progeny between X. hellerii and X. maculatus Jp163 A develop spontaneous melanoma initiating at the dorsal fin due to segregation of an oncogene and a regulator encoded by the X. maculatus genome, while the backcross hybrid progeny with X. hellerii or X. couchianus and Jp163 B exhibit melanoma on the flanks of their bodies, especially after treatment with ultraviolet light. Therefore, dissecting the genetic differences between these two closely related lines may lead to better understanding of functional molecular differences associated with tumorigenic mechanisms. For this purpose, comparative genomic analyses were undertaken to establish genetic variants between these two X. maculatus lines. Surprisingly, given the heritage of these two fish lines, we found genetic variants are clustered together in select chromosomal regions. Among these variants are non-synonymous mutations located in 381 genes. The non-random distribution of genetic variants between these two may highlight ancestral chromosomal recombination patterns that became fixed during subsequent inbreeding. Employing comparative transcriptomics, we also determined differences in the skin transcriptional landscape between the two lines. The genetic differences observed are associated with pathways highlighting fundamental cellular functions including inter-cellular and microenvironment-cellular interactions, and DNA repair. These results collectively lead to the conclusion that diverged functional genetic baselines are present between Jp163 A and B strains. Further, disruption of these fixed genetic baselines in the hybrids may give rise to spontaneous or inducible mechanisms of tumorigenesis.

Applications of Nanomaterials for Theranostics of Melanoma

Melanoma is an aggressive form of skin cancer with a very high mortality rate. Early diagnosis of the disease, the utilization of more potent pharmacological agents, and more effective drug delivery systems are essential to achieve an optimal treatment plan. The applications of nanotechnology to improve therapeutic efficacy and early diagnosis for melanoma treatment have received great interest among researchers and clinicians. In this review, we summarize the recent progress of utilizing various nanomaterials for theranostics of melanoma. The key importance of using nanomaterials for theranostics of melanoma is to improve efficacy and reduce side effects, ensuring safe implementation in clinical use. As opposed to conventional in vitro diagnostic methods, in vivo medical imaging technologies have the advantages of being a type of non-invasive, real-time monitoring. Several common nanoparticles, including ultrasmall superparamagnetic iron oxide nanoparticles, silica nanoparticles, and carbon-based nanoparticles, have been applied to deliver chemotherapeutic agents for the theranostics of melanoma. The application of nanomaterials for theranostics in molecular imaging (MRI, PET, US, OI, etc.) plays an important role in targeting drug delivery of melanoma, by monitoring the distribution site of the molecular imaging probe and the therapeutic drug in the body in real-time. Hence, it is worthwhile to anticipate the approval of these nanomaterials for theranostics in molecular imaging by the US Food and Drug Administration in clinical trials.

Genetic Engineering of Zebrafish in Cancer Research

Zebrafish (Danio rerio) is an excellent model to study a wide diversity of human cancers. In this review, we provide an overview of the genetic and reverse genetic toolbox allowing the generation of zebrafish lines that develop tumors. The large spectrum of genetic tools enables the engineering of zebrafish lines harboring precise genetic alterations found in human patients, the generation of zebrafish carrying somatic or germline inheritable mutations or zebrafish showing conditional expression of the oncogenic mutations. Comparative transcriptomics demonstrate that many of the zebrafish tumors share molecular signatures similar to those found in human cancers. Thus, zebrafish cancer models provide a unique in vivo platform to investigate cancer initiation and progression at the molecular and cellular levels, to identify novel genes involved in tumorigenesis as well as to contemplate new therapeutic strategies.

Development of germplasm repositories to assist conservation of endangered fishes: Examples from small-bodied livebearing fishes

Germplasm repositories are a necessary tool for comprehensive conservation programs to fully preserve valuable genetic resources of imperiled animals. Cryopreserved germplasm can be used in the future to produce live young for integration into other conservation projects, such as habitat restoration, captive breeding, and translocations; thus compensating for genetic losses or negative changes that would otherwise be permanent. Although hundreds of cryopreservation protocols for various aquatic species have been published, there are great difficulties in moving such research forward into applied conservation projects. Successful freezing of sperm in laboratories for research does not guarantee successful management and incorporation of genetic resources into conservation programs in reality. The goal of the present review is to provide insights and practical strategies to apply germplasm repositories as a real-world tool to assist conservation of imperiled aquatic species. Live-bearing (viviparous) fishes are used as models herein to help explain concepts because they are good examples for aquatic species in general, especially small-bodied fishes. Small live-bearing fishes are among the most at-risk fish groups in the world, and need urgent conservation attention. However, development of germplasm repositories for small live-bearing fishes is challenged by their unusual reproductive characteristics, such as formation of sperm bundles, initiation of spermatozoa motility in an isotonic environment, internal fertilization and gestation, and the bearing of live young. The development of germplasm repositories for goodeids and Xiphophorus species can provide examples for addressing these challenges. Germplasm repositories must contain multiple basic components, including frozen samples, genetic assessment and information systems. Standardization and process generalization are important strategies to help develop reliable and efficient repositories. An ideal conservation or recovery program for imperiled species should include a comprehensive approach, that combines major concerns such as habitat (by restoration projects), population propagation and maintenance (by captive breeding or translocation projects), and preservation of genetic diversity (by repository projects). In this context, strong collaboration among different sectors and people with different expertise is a key to the success of such comprehensive programs.

Immunohistochemical Study of Four Fish Tumors

The present study supports the usefulness of ancillary techniques, such as immunohistochemistry, as a valid diagnostic tool in the field of fish oncology. The immunohistochemical patterns observed in four neoplasms on four individual teleosts belonging to different species are described. Cytokeratin, vimentin, actin, S100, calretinin, and Melan-A antibodies were used. Diagnoses of papilloma in a Bream Abramis brama, fibroma in a Sand Steenbras Lithognathus mormyrus, schwannoma in a Crucian Carp Carassius carassius, and melanoma in a spontaneously inbred Xiphophorus hybrid were made. Diagnosis of tumors in fish is not always easy to carry out, and the tool provided by antibodies used on mammalian tissue is essential for obtaining definitive, unambiguous, and inexpensive identification.

Workshop report: Cryopreservation of aquatic biomedical models

The genetic resources of aquatic biomedical model organisms are the products of millions of years of evolution, decades of scientific development, and hundreds of millions of dollars of research funding investment. Genetic resources (e.g., specific alleles, transgenes, or combinations) of each model organism can be considered a form of scientific wealth that can be accumulated and exchanged, typically in the form of live animals or germplasm. Large-scale maintenance of live aquatic organisms that carry these genetic resources is inefficient, costly, and risky. In situ maintenance may be substantially enhanced and backed up by combining cryopreserved germplasm repositories and genetic information systems with live animal culture. Unfortunately, cryopreservation has not advanced much beyond the status of an exploratory research for most aquatic species, lacks widespread application, and methods for successful cryopreservation remain poorly defined. For most aquatic species biological materials other than sperm or somatic cells are not comprehensively banked to represent and preserve a broad range of genetic diversity for each species. Therefore, new approaches and standardization are needed for repository-level application to ensure reproducible recovery of cryopreserved materials. Additionally, development of new technologies is needed to address preservation of novel biological materials, such as eggs and embryos of aquatic species. To address these goals, the Office of Research Infrastructure Programs (ORIP) of the National Institutes of Health (NIH) hosted the Cryopreservation of Aquatic Biomedical Models Workshop on January 7 to 8, 2017, in conjunction with the 8th Aquatic Animal Models of Human Disease Conference in Birmingham, Alabama. The goals of the workshop were to assess the status of germplasm cryopreservation in various biomedical aquatic models and allow representatives of the scientific community to develop and prioritize a consensus of specific actionable recommendations that will move the field of cryopreservation of aquatic resources forward. This workshop included sessions devoted to new approaches for cryopreservation of aquatic species, discussion of current efforts and approaches in preservation of aquatic model germplasm, consideration of needs for standardization of methods to support reproducibility, and enhancement of repository development by establishment of scalable high-throughput technologies. The following three broad recommendations were forwarded from workshop attendees: 1: Establish a comprehensive, centralized unit ("hub") to programmatically develop training for and documentation of cryopreservation methods for aquatic model systems. This would include development of species-specific protocols and approaches, outreach programs, community development and standardization, freezing services and training of the next generation of experts in aquatic cryopreservation. 2: Provide mechanisms to support innovative technical advancements that will increase the reliability, reproducibility, simplicity, throughput, and efficiency of the cryopreservation process, including vitrification and pipelines for sperm, oocytes, eggs, embryos, larvae, stem cells, and somatic cells of all aquatic species. This recommendation encompasses basic cryopreservation knowledge and engineering technology, such as microfluidics and automated processing technologies. 3: Implement mechanisms that allow the various aquatic model stock centers to increase their planning, personnel, ability to secure genetic resources and to promote interaction within an integrated, comprehensive repository network for aquatic model species repositories.

Comparison of Xiphophorus and human melanoma transcriptomes reveals conserved pathway interactions

Comparative analysis of human and animal model melanomas can uncover conserved pathways and genetic changes that are relevant for the biology of cancer cells. Spontaneous melanoma in Xiphophorus interspecies backcross hybrid progeny may be informative in identifying genes and functional pathways that are similarly related to melanoma development in all vertebrates, including humans. To assess functional pathways involved in the Xiphophorus melanoma, we performed gene expression profiling of the melanomas produced in interspecies BC1 and successive backcross generations (i.e., BC5 ) of the cross: X. hellerii × [X. maculatus Jp 163 A × X. hellerii]. Using RNA-Seq, we identified genes that are transcriptionally co-expressed with the driver oncogene, xmrk. We determined functional pathways in the fish melanoma that are also present in human melanoma cohorts that may be related to dedifferentiation based on the expression levels of pigmentation genes. Shared pathways between human and Xiphophorus melanomas are related to inflammation, cell migration, cell proliferation, pigmentation, cancer development, and metastasis. Our results suggest xmrk co-expressed genes are associated with dedifferentiation and highlight these signaling pathways as playing important roles in melanomagenesis.

Production of live young with cryopreserved sperm from the endangered livebearing fish Redtail Splitfin (Xenotoca eiseni, Rutter, 1896)

Previous studies of sperm cryopreservation of livebearing fish have been limited to two genera within the family Poeciliidae. The goal of the present study was to investigate the feasibility to produce live young of livebearing goodeids (family Goodeidae) with cryopreserved sperm, using aquarium-trade populations of the endangered species Redtail Splitfin (Xenotoca eiseni, Rutter, 1896). Reproductive condition of females was evaluated by histological categorization of ovarian development. A total of 117 females were inseminated with cryopreserved sperm, 81 were inseminated with fresh sperm, 27 were mixed with males for natural breeding, and 30 were maintained without males or insemination. Histological images of 34 mature females indicated 68% of ovaries had primary- or secondary-growth oocytes, and 32% had ovulated eggs. Ovarian development had no significant relationship (P =  0.508) with body wet weight, but had a relationship (P <  0.001) with ovary weight and gonadosomatic index. Sperm cells were observed within ovaries that were fixed at 12 h after insemination with fresh sperm. A total of 29 live young were produced from two females inseminated with thawed sperm (8% post-thaw motility with HBSS300 as extender, 20 min incubation in 15% DMSO, cooling rate at 10 °C/min, and thawing at 40 °C for 7 s), 12 were produced from two females with fresh sperm (1%-20% motility), 41 were produced from five naturally spawned females, and no live young were produced from the female-only group. This study provides a foundation for establishment of germplasm repositories for endangered goodeids to assist conservation programs.

The transcriptional response of skin to fluorescent light exposure in viviparous (Xiphophorus) and oviparous (Danio, Oryzias) fishes

Differences in light sources are common in animal facilities and potentially can impact experimental results. Here, the potential impact of lighting differences on skin transcriptomes has been tested in three aquatic animal models commonly utilized in biomedical research, (Xiphophorus maculatus (platyfish), Oryzias latipes (medaka) and Danio rerio (zebrafish). Analysis of replicate comparative RNA-Seq data showed the transcriptional response to commonly utilized 4100K or "cool white" fluorescent light (FL) is much greater in platyfish and medaka than in zebrafish. FL induces genes associated with inflammatory and immune responses in both medaka and zebrafish; however, the platyfish exhibit suppression of genes involved with immune/inflammation, as well as genes associated with cell cycle progression. Furthermore, comparative analyses of gene expression data from platyfish UVB exposures, with medaka and zebrafish after exposure to 4100K FL, show comparable effects on the same stress pathways. We suggest the response to light is conserved, but that long-term adaptation to species specific environmental niches has resulted in a shifting of the wavelengths required to incite similar "genetic" responses in skin. We forward the hypothesis that the "genetic perception" of light may have evolved differently than ocular perception and suggest that light type (i.e., wavelengths emitted) is an important parameter to consider in experimental design.

Innovative Disease Model: Zebrafish as an In Vivo Platform for Intestinal Disorder and Tumors

Colorectal cancer (CRC) is one of the world’s most common cancers and is the second leading cause of cancer deaths, causing more than 50,000 estimated deaths each year. Several risk factors are highly associated with CRC, including being overweight, eating a diet high in red meat and over-processed meat, having a history of inflammatory bowel disease, and smoking. Previous zebrafish studies have demonstrated that multiple oncogenes and tumor suppressor genes can be regulated through genetic or epigenetic alterations. Zebrafish research has also revealed that the activation of carcinogenesis-associated signal pathways plays an important role in CRC. The biology of cancer, intestinal disorders caused by carcinogens, and the morphological patterns of tumors have been found to be highly similar between zebrafish and humans. Therefore, the zebrafish has become an important animal model for translational medical research. Several zebrafish models have been developed to elucidate the characteristics of gastrointestinal diseases. This review article focuses on zebrafish models that have been used to study human intestinal disorders and tumors, including models involving mutant and transgenic fish. We also report on xenograft models and chemically-induced enterocolitis. This review demonstrates that excellent zebrafish models can provide novel insights into the pathogenesis of gastrointestinal diseases and help facilitate the evaluation of novel anti-tumor drugs.

Molecular genetic analysis of the melanoma regulatory locus in Xiphophorus interspecies hybrids

Development of spontaneous melanoma in Xiphophorus interspecies backcross hybrid progeny, (X. hellerii × [X. maculatus Jp 163 A × X. hellerii]) is due to Mendelian segregation of a oncogene (xmrk) and a molecularly uncharacterized locus, called R(Diff), on LG5. R(Diff) is thought to suppresses the activity of xmrk in healthy X. maculatus Jp 163 A parental species that rarely develop melanoma. To better understand the molecular genetics of R(Diff), we utilized RNA-Seq to study allele-specific gene expression of spontaneous melanoma tumors and corresponding normal skin samples derived from 15 first generation backcross (BC₁ ) hybrids and 13 fifth generation (BC₅ ) hybrids. Allele-specific expression was determined for all genes and assigned to parental allele inheritance for each backcross hybrid individual. Results showed that genes residing in a 5.81 Mbp region on LG5 were exclusively expressed from the X. hellerii alleles in tumor-bearing BC₁ hybrids. This observation indicates this region is consistently homozygous for X. hellerii alleles in tumor bearing animals, and therefore defines this region to be the R(Diff) locus. The R(Diff) locus harbors 164 gene models and includes the previously characterized R(Diff) candidate, cdkn2x. Twenty-one genes in the R(Diff) region show differential expression in the tumor samples compared to normal skin tissue. These results further characterize the R(Diff) locus and suggest tumor suppression may require a multigenic region rather than a single gene variant. Differences in gene expression between tumor and normal skin tissue in this region may indicate interactions among several genes are required for backcross hybrid melanoma development.

Xiphophorus and Medaka Cancer Models

Besides recently developed zebrafish cancer models, other fish species have been employed for many years as cancer models in laboratory studies. Two models, namely in Xiphophorus and medaka have proven useful in providing important clues to cancer etiology. Medaka is a complementary model to zebrafish in many areas of research since it offers similar resources and experimental tools. Xiphophorus provides the advantages of a natural ("evolutionary mutant") model with established genetics. Xiphophorus hybrids can develop spontaneous and radiation or carcinogen induced cancers. This chapter describes the tumor models in both species, which mainly focus on melanoma, and summarizes the main findings and future research directions.

X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species

BACKGROUND

Xiphophorus fishes are represented by 26 live-bearing species of tropical fish that express many attributes (e.g., viviparity, genetic and phenotypic variation, ecological adaptation, varied sexual developmental mechanisms, ability to produce fertile interspecies hybrids) that have made attractive research models for over 85 years. Use of various interspecies hybrids to investigate the genetics underlying spontaneous and induced tumorigenesis has resulted in the development and maintenance of pedigreed Xiphophorus lines specifically bred for research. The recent availability of the X. maculatus reference genome assembly now provides unprecedented opportunities for novel and exciting comparative research studies among Xiphophorus species.

RESULTS

We present sequencing, assembly and annotation of two new genomes representing Xiphophorus couchianus and Xiphophorus hellerii. The final X. couchianus and X. hellerii assemblies have total sizes of 708 Mb and 734 Mb and correspond to 98 % and 102 % of the X. maculatus Jp 163 A genome size, respectively. The rates of single nucleotide change range from 1 per 52 bp to 1 per 69 bp among the three genomes and the impact of putatively damaging variants are presented. In addition, a survey of transposable elements allowed us to deduce an ancestral TE landscape, uncovered potential active TEs and document a recent burst of TEs during evolution of this genus.

CONCLUSIONS

Two new Xiphophorus genomes and their corresponding transcriptomes were efficiently assembled, the former using a novel guided assembly approach. Three assembled genome sequences within this single vertebrate order of new world live-bearing fishes will accelerate our understanding of relationship between environmental adaptation and genome evolution. In addition, these genome resources provide capability to determine allele specific gene regulation among interspecies hybrids produced by crossing any of the three species that are known to produce progeny predisposed to tumor development.

Transcriptional control analyses of the Xiphophorus melanoma oncogene

Melanoma development in interspecific hybrids of Xiphophorus is induced by the overexpression of the mutationally activated receptor tyrosine kinase Xmrk in pigment cells. Based on the melanocyte specificity of the transcriptional upregulation, a pigment cell-specific promoter region was postulated for xmrk, the activity of which is controlled in healthy purebred fish by the molecularly still unidentified regulator locus R. However, as yet the xmrk promoter region is still poorly characterized. In order to contribute to a better understanding of xmrk expression regulation, we performed a functional analysis of the entire putative gene regulatory region of the oncogene using conventional plasmid-based reporter systems as well as a newly established method employing BAC-derived luciferase reporter constructs in melanoma and non-melanoma cell lines. Using the melanocyte-specific mitfa promoter as control, we could demonstrate that our in vitro system is able to reliably monitor regulation of transcription through cell type-specific regulatory sequences. We found that sequences within 200kb flanking the xmrk oncogene do not lead to any specific transcriptional activation in melanoma compared to control cells. Hence, xmrk reporter constructs fail to faithfully reproduce the endogenous transcriptional regulation of the oncogene. Our data therefore strongly indicate that the melanocyte-specific transcription of xmrk is not the consequence of pigment cell-specific cis-regulatory elements in the promoter region. This hints at additional regulatory mechanisms involved in transcriptional control of the oncogene, thereby suggesting a key role for epigenetic mechanisms in oncogenic xmrk overexpression and thereby in tumor development in Xiphophorus.

Sex-specific molecular genetic response to UVB exposure in Xiphophorus maculatus skin

In both Xiphophorus fishes and humans, males are reported to have a higher incidence of melanoma than females. To better understand sex-specific differences in the molecular genetic response to UVB, we performed RNA-Seq experiments in skin of female and male Xiphophorus maculatus Jp 163 B following UVB doses of 8 or 16kJ/m(2) exposure. Male X. maculatus differentially express a significantly larger number of transcripts following exposure to 16kJ/m(2) UVB (1293 genes) compared to 8kJ/m(2) UVB (324 genes). Female skin showed differential gene expression in a larger number of transcripts following 8kJ/m(2) UVB (765) than did males; however, both females and males showed similar numbers of differentially expressed genes at 16kJ/m(2) UVB (1167 and1293, respectively). Although most modulated transcripts after UVB exposure represented the same dominant pathways in both females and males (e.g., DNA repair, circadian rhythm, and fatty acid biosynthesis), we identified genes in several pathways that exhibited opposite modulation in female vs. male skin (e.g., synaptic development, cell differentiation, wound healing, and glucose metabolism). The oppositely modulated genes appear related through uncoupling protein 3 (UCP3) that is involved with the regulation of fatty acid oxidation and serves to balance glucose and lipid metabolism. Overall, these results identify gender-specific differences in UVB-induced genetic profiles in the skin of females and males and show female and male X. maculatus respond to UVB differently through pathways involved in reactive oxygen species, wound healing, and energy homeostasis.

Molecular genetic response of Xiphophorus maculatus-X. couchianus interspecies hybrid skin to UVB exposure

The phenotypic and genetic similarities between Xiphophorus and human melanoma render Xiphophorus a useful animal model for studying the genetic basis of melanoma etiology. In the Xiphophorus model, melanoma has been shown to be inducible by ultraviolet light (UVB) exposure among interspecies hybrids, but not in parental line fish similarly treated. This leads to questions of what genes are responsive to UVB exposure in the skin of the interspecies hybrids, as well as how parental alleles in hybrids may be differentially regulated and the potential roles they may play in induced melanomagenesis. To address these questions, we produced X. maculatus Jp 163 B×X. couchianus (Sp-Couch) F1 hybrid fish, exposed both hybrid and parental fish to UVB, and performed gene expression profiling of the skin using RNA-Seq methodology. We characterized a group of unique UVB-responsive genes in Sp-Couch hybrid including dct, pmela, tyr, tyrp1a, slc2a11b, rab38a, rab27, tspan10, slc45a2, oca2, slc24a5, ptn and mitfa. These genes are associated with melanin production and melanocyte proliferation. They were also up-regulated in Sp-Couch hybrid, indicating that their UVB response is hybridization initiated. In the hybrid, several melanin production and pigmentation related genes, including slc45a2, tspan10, dct, slc2a11b and ptn showed either X. couchianus or X. maculatus allele specific expression. The finding that these genes exhibit allele specific expression regulatory mechanisms in Sp-Couch hybrids, but do not exhibit a corresponding UVB response in either one of the parental fishes, may suggest UVB targets and imply mechanisms regarding the susceptibility of Sp-Couch to induced melanomagenesis.

Characterization and differential expression of CPD and 6-4 DNA photolyases in Xiphophorus species and interspecies hybrids

Among the many Xiphophorus interspecies hybrid tumor models are those that exhibit ultraviolet light (UVB) induced melanoma. In previous studies, assessment of UVB induced DNA damage and nucleotide excision DNA repair has been performed in parental lines and interspecies hybrids. Species and hybrid specific differences in the levels of DNA damage induced and the dark repair rates for cyclobutane pyrimidine dimers (CPDs) and 6-4 pyrimidine pyrimidine photoproducts (6-4PPs) have been reported. However, UVB induced DNA lesions in Xiphophorus fishes are thought to primarily be repaired via light dependent CPD and 6-4PP specific photolyases. Photolyases are of evolutionary interest since they are ancient and presumably function solely to ameliorate the deleterious effects of UVB exposure. Herein, we report results from detailed studies of CPD and 6-4PP photolyase gene expression within several Xiphophorus tissues. We determined photolyase gene expression patterns before and after exposure to fluorescent light in X. maculatus, X. couchianus, and for F1 interspecies hybrids produced from crossing these two parental lines (X. maculatus Jp 163 B×X. couchianus). We present novel results showing these two photolyase genes exhibit species, tissue, and hybrid-specific differences in basal and light induced gene expression.

UVB-induced gene expression in the skin of Xiphophorus maculatus Jp 163 B

Xiphophorus fish and interspecies hybrids represent long-standing models to study the genetics underlying spontaneous and induced tumorigenesis. The recent release of the Xiphophorus maculatus genome sequence will allow global genetic regulation studies of genes involved in the inherited susceptibility to UVB-induced melanoma within select backcross hybrids. As a first step toward this goal, we report results of an RNA-Seq approach to identify genes and pathways showing modulated transcription within the skin of X. maculatus Jp 163 B upon UVB exposure. X. maculatus Jp 163 B were exposed to various doses of UVB followed by RNA-Seq analysis at each dose to investigate overall gene expression in each sample. A total of 357 genes with a minimum expression change of 4-fold (p-adj<0.05) were identified as responsive to UVB. The molecular genetic response of Xiphophorus skin to UVB exposure permitted assessment of; (1) the basal expression level of each transcript for each skin sample, (2) the changes in expression levels for each gene in the transcriptome upon exposure to increasing doses of UVB, and (3) clusters of genes that exhibit similar patterns of change in expression upon UVB exposure. These data provide a foundation for understanding the molecular genetic response of fish skin to UVB exposure.

Targeting events in melanoma carcinogenesis for the prevention of melanoma

Melanoma is one of the few tumors that have increased in incidence over the last few decades. Strategies devoted solely to protecting against ultraviolet radiation have, at best, had a modest impact on the development of melanoma. Chemoprevention is an under-explored approach that could significantly decrease the morbidity and mortality from this deadly cancer. However, the scientific and logistical challenges of performing clinical studies in chemoprevention require innovative approaches to prove the effectiveness of putative preventive agents. There are several pharmacological and nutriceutical agents that are mechanistically linked to events in melanoma carcinogenesis that are candidates for advanced human studies. We will review the data for several promising agents, including statins, curcumin, resveratrol, silymarin and green tea, and discuss some importance issues and concepts that should be considered in any melanoma chemoprevention strategy.

Evaluation of polycyclic aromatic hydrocarbons using analytical methods, toxicology, and risk assessment research: seafood safety after a petroleum spill as an example

BACKGROUND

Polycyclic aromatic hydrocarbons (PAHs) are abundant and widespread environmental chemicals. They are produced naturally and through man-made processes, and they are common in organic media, including petroleum. Several PAHs are toxic, and a subset exhibit carcinogenic activity. PAHs represent a range of chemical structures based on two or more benzene rings and, depending on their source, can exhibit a variety of side modifications resulting from oxygenation, nitrogenation, and alkylation.

OBJECTIVES

Here we discuss the increasing ability of contemporary analytical methods to distinguish not only different chemical structures among PAHs but also their concentrations in environmental media. Using seafood contamination following the Deepwater Horizon accident as an example, we identify issues that are emerging in the PAH risk assessment process because of increasing analytical sensitivity for individual PAHs, and we describe the paucity of toxicological literature for many of these compounds.

DISCUSSION

PAHs, including the large variety of chemically modified or substituted PAHs, are naturally occurring and may constitute health risks if human populations are exposed to hazardous levels. However, toxicity evaluations have not kept pace with modern analytic methods and their increased ability to detect substituted PAHs. Therefore, although it is possible to measure these compounds in seafood and other media, we do not have sufficient information on the potential toxicity of these compounds to incorporate them into human health risk assessments and characterizations.

CONCLUSIONS

Future research efforts should strategically attempt to fill this toxicological knowledge gap so human health risk assessments of PAHs in environmental media or food can be better determined. This is especially important in the aftermath of petroleum spills.

Modeling Melanoma In Vitro and In Vivo

The behavior of melanoma cells has traditionally been studied in vitro in two-dimensional cell culture with cells adhering to plastic dishes. However, in order to mimic the three-dimensional architecture of a melanoma, as well as its interactions with the tumor microenvironment, there has been the need for more physiologically relevant models. This has been achieved by designing 3D in vitro models of melanoma, such as melanoma spheroids embedded in extracellular matrix or organotypic skin reconstructs. In vivo melanoma models have typically relied on the growth of tumor xenografts in immunocompromised mice. Several genetically engineered mouse models have now been developed which allow the generation of spontaneous melanoma. Melanoma models have also been established in other species such as zebrafish, which are more conducive to imaging and high throughput studies. We will discuss these models as well as novel techniques that are relevant to the study of the molecular mechanisms underlying melanoma progression.

Beyond the zebrafish: diverse fish species for modeling human disease

In recent years, zebrafish, and to a lesser extent medaka, have become widely used small animal models for human diseases. These organisms have convincingly demonstrated the usefulness of fish for improving our understanding of the molecular and cellular mechanisms leading to pathological conditions, and for the development of new diagnostic and therapeutic tools. Despite the usefulness of zebrafish and medaka in the investigation of a wide spectrum of traits, there is evidence to suggest that other fish species could be better suited for more targeted questions. With the emergence of new, improved sequencing technologies that enable genomic resources to be generated with increasing efficiency and speed, the potential of non-mainstream fish species as disease models can now be explored. A key feature of these fish species is that the pathological condition that they model is often related to specific evolutionary adaptations. By exploring these adaptations, new disease-causing and disease-modifier genes might be identified; thus, diverse fish species could be exploited to better understand the complexity of disease processes. In addition, non-mainstream fish models could allow us to study the impact of environmental factors, as well as genetic variation, on complex disease phenotypes. This Review will discuss the opportunities that such fish models offer for current and future biomedical research.

Using PET/CT imaging to characterize 18 F-fluorodeoxyglucose utilization in fish

Fish are becoming an increasingly important research species as investigators seek alternatives to mammalian models. Combined positron emission tomography/computed tomography with ¹⁸F-fluorodeoxyglucose (FDG-PET/CT) is a powerful new technology that has been extensively applied for high-resolution imaging in mammals but not fish. CT scanning provides detailed anatomical three-dimensional imaging. PET scanning detects areas of cellular activity using radio-labelled molecular probes with specific uptake rates appropriate to the tissue involved. FDG-PET is used in oncology because tissues with high glucose uptake, such as neoplasms, are intensely radio-labelled. PET/CT combines the two technologies, so that images acquired from both devices are merged into one superimposed image, thus more precisely correlating metabolic activity with anatomical three-dimensional imaging. Our objective was to determine if fish can be viable replacement animals in cancer studies using this technique by analysing the similarities between fish and humans in glucose uptake in select organs across multiple fish species. Rapid, quantifiable glucose uptake was demonstrated, particularly in brain, kidneys and liver in all imaged fish species. Standard uptake values for glucose uptake in the major organ systems of fish were more similar to those of humans than mice or dogs, indicating that fish may serve as effective alternative animal models using this technology. Applications for this technique in fish may include oncogenesis and metabolism studies as well as screening for environmental carcinogenesis.

Neoplasia and neoplasm-associated lesions in laboratory colonies of zebrafish emphasizing key influences of diet and aquaculture system design

During the past decade, the zebrafish has emerged as a leading model for mechanistic cancer research because of its sophisticated genetic and genomic resources, its tractability for tissue targeting of transgene expression, its efficiency for forward genetic approaches to cancer model development, and its cost effectiveness for enhancer and suppressor screens once a cancer model is established. However, in contrast with other laboratory animal species widely used as cancer models, much basic cancer biology information is lacking in zebrafish. As yet, data are not published regarding dietary influences on neoplasm incidences in zebrafish. Little information is available regarding spontaneous tumor incidences or histologic types in wild-type lines of zebrafish. So far, a comprehensive database documenting the full spectrum of neoplasia in various organ systems and tissues is not available for zebrafish as it is for other intensely studied laboratory animal species. This article confirms that, as in other species, diet and husbandry can profoundly influence tumor incidences and histologic spectra in zebrafish. We show that in many laboratory colonies wild-type lines of zebrafish exhibit elevated neoplasm incidences and neoplasm-associated lesions such as heptocyte megalocytosis. We present experimental evidence showing that certain diet and water management regimens can result in high incidences of neoplasia and neoplasm-associated lesions. We document the wide array of benign and malignant neoplasms affecting nearly every organ, tissue, and cell type in zebrafish, in some cases as a spontaneous aging change, and in other cases due to carcinogen treatment or genetic manipulation.

The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits

Several attributes intuitively considered to be typical mammalian features, such as complex behavior, live birth, and malignant diseases like cancer, also appeared several times independently in so-called “lower” vertebrates. The genetic mechanisms underlying the evolution of these elaborate traits are poorly understood. The platyfish, Xiphophorus maculatus, offers a unique model to better understand the molecular biology of such traits. Herein we detail sequencing of the platyfish genome. Integrating genome assembly with extensive genetic maps uncovered that fish, in contrast to mammals, exhibit an unexpected evolutionary stability of chromosomes. Genes associated with viviparity show signatures of positive selection identifying new putative functional domains and rare cases of parallel evolution. We also discovered that genes implicated in cognition possess an unexpected high rate of duplicate gene retention after the teleost genome duplication suggesting a hypothesis for the evolution of the great behavioral complexity in fish, which exceeds that in amphibians and reptiles.

Sperm cryopreservation in live-bearing Xiphophorus fishes: offspring production from Xiphophorus variatus and strategies for establishment of sperm repositories

Cryopreservation of sperm from Xiphophorus fishes has produced live young in three species: X. hellerii, X. couchianus, and X. maculatus. In this study, the goal was to establish protocols for sperm cryopreservation and artificial insemination to produce live young in X. variatus, and to identify needs for repository development. The objectives were to: 1) collect basic biological characteristics of males; 2) cryopreserve sperm from X. variatus, 3) harvest live young from cryopreserved sperm, and 4) discuss the requirements for establishment of sperm repositories. The 35 males used in this study had a body weight of 0.298±0.096 g (mean±SD), body length of 2.5±0.2 cm, and testis weight of 6.4±3.4 mg. The sperm production per gram of testis was 2.33±1.32×10(9) cells. After freezing, the post-thaw motility decreased significantly to 37%±17% (ranging from 5% to 70%) (p=0.000) from 57%±14% (40%-80%) of fresh sperm (N=20). Artificial insemination of post-thaw sperm produced confirmed offspring from females of X. hellerii and X. variatus. This research, taken together with previous studies, provides a foundation for development of strategies for sperm repositories of Xiphophorus fishes. This includes: 1) the need for breeding strategies for regeneration of target populations, 2) identification of minimum fertilization capacity of frozen samples, 3) identification of fish numbers necessary for sampling and their genetic relationships, 4) selection of packaging containers for labeling and biosecurity, 5) assurance of quality control and standardization of procedures, 6) information systems that can manage the data associated with cryopreserved samples, including the genetic data, 7) biological data of sampled fish, 8) inventory data associated with frozen samples, and 9) data linking germplasm samples with other related materials such as body tissues or cells saved for DNA and RNA analyses.

Identification of transcriptome SNPs between Xiphophorus lines and species for assessing allele specific gene expression within F₁ interspecies hybrids

Variations in gene expression are essential for the evolution of novel phenotypes and for speciation. Studying allelic specific gene expression (ASGE) within interspecies hybrids provides a unique opportunity to reveal underlying mechanisms of genetic variation. Using Xiphophorus interspecies hybrid fishes and high-throughput next generation sequencing technology, we were able to assess variations between two closely related vertebrate species, Xiphophorus maculatus and Xiphophorus couchianus, and their F(1) interspecies hybrids. We constructed transcriptome-wide SNP polymorphism sets between two highly inbred X. maculatus lines (JP 163 A and B), and between X. maculatus and a second species, X. couchianus. The X. maculatus JP 163 A and B parental lines have been separated in the laboratory for ≈70 years and we were able to identify SNPs at a resolution of 1 SNP per 49 kb of transcriptome. In contrast, SNP polymorphisms between X. couchianus and X. maculatus species, which diverged ≈5-10 million years ago, were identified about every 700 bp. Using 6524 transcripts with identified SNPs between the two parental species (X. maculatus and X. couchianus), we mapped RNA-seq reads to determine ASGE within F(1) interspecies hybrids. We developed an in silico X. couchianus transcriptome by replacing 90,788 SNP bases for X. maculatus transcriptome with the consensus X. couchianus SNP bases and provide evidence that this procedure overcomes read mapping biases. Employment of the in silico reference transcriptome and tolerating 5 mismatches during read mapping allow direct assessment of ASGE in the F(1) interspecies hybrids. Overall, these results show that Xiphophorus is a tractable vertebrate experimental model to investigate how genetic variations that occur during speciation may affect gene interactions and the regulation of gene expression.

Offspring production with cryopreserved sperm from a live-bearing fish Xiphophorus maculatus and implications for female fecundity

Xiphophorus fishes are well-established models for biomedical research of spontaneous or induced tumors, and their use in research dates back to the 1930s. Currently, 58 well-pedigreed lines exist among 24 Xiphophorus species housed as live animals at the Xiphophorus Genetic Stock Center. The technique of sperm cryopreservation has been applied to preserve these valuable genetic resources, and production of offspring has been reported with cryopreserved sperm in two species (X. helleri and X. couchianus). The goal of this research was to establish protocols for sperm cryopreservation and artificial insemination that yield live young in X. maculatus, a widely used research species. The objectives were to: 1) collect basic biological characteristics of males, and quantify the sperm production yield after crushing of dissected testis; 2) cryopreserve sperm from X. maculatus by adapting as necessary the protocols for sperm cryopreservation of X. helleri and X. couchianus; 3) use cryopreserved sperm to inseminate virgin females of X maculatus and other species (X. helleri and X. couchianus), and 4) compare experimental trials over a 3-year period to identify opportunities for improving female fecundity. In total, 117 males were used in this study with a standard length of 2.5 ± 0.3 cm (mean ± SD), body weight of 0.474 ± 0.149 g, and dissected testis weight of 7.1 ± 3.7 mg. Calculation of sperm availability showed 5.9 ± 2.8 × 10(6) sperm cells per mg of testis weight. Offspring were produced from cryopreserved sperm. Male-to-male variation (1-70%) was observed in post-thaw motility despite little variation in motility before freezing (60-90%) or genetic variation (~100 generations of sib-mating). Comparisons of biological factors of males did not have significant correlations with the production of live young, and the influence of females on production of young was identified from the comparison of artificial insemination over 3 years. Overall, this study describes offspring production from cryopreserved sperm in a third species of Xiphophorus fishes, and identifies the opportunities for improving female fecundity which is essential for establishment of germplasm repositories for Xiphophorus fishes.

Characterization of telomeres and telomerase expression in Xiphophorus

Research investigating telomere lengths and telomerase expression in vertebrates has progressively become important due to the association of these two biological endpoints with cellular aging and cancer in humans. Studies that rely upon the traditional use of laboratory mice have been faced with limitations largely due to inbred mice possessing large telomeres and ubiquitous expression of telomerase. Recently, a number of small fish species have been shown to provide potentially informative models for examining the role of telomeres and telomerase within intact vertebrate animals. Xiphophorus fishes represent a new world live-bearing genus that has not previously been assessed for telomere length or telomerase expression. To add to the knowledge base of telomere and telomerase biology in vertebrates we assessed telomere length and telomerase expression among several species of Xiphophorus. The telomere lengths in several organs (gill, brain, eyes, testis, ovary and liver) in three species (Xiphophorus hellerii, Xiphophorus maculatus, Xiphophorus couchianus) and also in F(1) interspecies hybrids were approximately 2-6 kb. This size was consistent within the same organs of the same species, as well as between species and F(1) hybrids. Despite possessing relatively short telomere lengths compared to humans, the consistency of size among Xiphophorus species and organs may allow experimental detection of telomere shortening. The relative expression of telomerase reverse transcriptase (TERT) was determined by quantitative real-time PCR. Expression levels of TERT was measured in seven organs (ovary, testis, liver, gill, brain, heart, skin) from X. maculatus, X. hellerii and in control and ultraviolet light (UVB) exposed skin samples from X. maculatus, X. hellerii, and F(1) interspecies hybrids. TERT gene expression was significantly higher in ovary and testis, while all other organs showed low relative TERT expression. Detectable increases in TERT expression were found in skin samples upon UVB exposure. Our findings suggest that Xiphophorus may serve as a suitable model for future studies investigating the association of telomere length and telomerase expression in regard to aging and disease.

Chemoprevention of melanoma

Despite advances in drug discovery programs and molecular approaches for identifying drug targets, incidence and mortality rates due to melanoma continue to rise at an alarming rate. Existing preventive strategies generally involve mole screening followed by surgical removal of the benign nevi and abnormal moles. However, due to lack of effective programs for screening and disease recurrence after surgical resection, there is a need for better chemopreventive agents. Although sunscreens have been used extensively for protecting from UV-induced melanomas, results of correlative population-based studies are controversial, with certain studies suggest increased skin cancer risk in sunscreen users. Therefore, these studies require further authentication to conclusively confirm the chemoprotective efficacy of sunscreens. This chapter reviews the current understanding regarding melanoma chemoprevention and the various strategies used to accomplish this objective.

One step forward: the use of transgenic zebrafish tumor model in drug screens

The zebrafish (Danio rerio) has been an experimental model in the developmental biology and toxicology since the 1950s. In recent years, with the aid of transgenic technology, it has also gained an increasing popularity to model human diseases, including various cancers. As a feasible vertebrate model for large-scale chemical screens, the zebrafish has also given us a new option for the search of potential anticancer drugs. It is hopeful that in the near future with automation and analytical tools, drug development processes will be significantly shortened for quick and effective identification of candidate drugs.

Transcriptome analysis of female and male Xiphophorus maculatus Jp 163 A

Background

Xiphophorus models are important for melanoma, sex determination and differentiation, ovoviviparity and evolution. To gain a global view of the molecular mechanism(s) whereby gene expression may influence sexual dimorphism in Xiphophorus and to develop a database for future studies, we performed a large-scale transcriptome study.

Methodology/Principal Findings

The 454-FLX massively parallel DNA sequencing platform was employed to obtain 742,771 and 721,543 reads from 2 normalized cDNA libraries generated from whole adult female and male X. maculatus Jp 163 A, respectively. The reads assembled into 45,538 contigs (here, a "contig" is a set of contiguous sequences), of which, 11,918 shared homology to existing protein sequences. These numbers estimate that the contigs may cover 53% of the total number of Xiphophorus transcriptome. Putative translations were obtained for 11,918 cDNA contigs, of which, 3,049 amino acid sequences contain Pfam domains and 11,064 contigs encode secretory proteins. A total of 3,898 contigs were associated with 2,781 InterPro (IPR) entries and 5,411 contigs with 132 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. There were 10,446 contigs annotated with 69,778 gene ontology (GO) terms and the three corresponding organizing principles. Fifty-four potential sex differentially expressed genes have been identified from these contigs. Eight and nine of these contigs were confirmed by real-time PCR as female and male predominantly expressed genes respectively. Based on annotation results, 34 contigs were predicted to be differentially expressed in male and female and 17 of them were also confirmed by real-time PCR.

Conclusions/Significance

This is the first report of an annotated overview of the transcriptome of X. maculatus and identification of sex differentially expressed genes. These data will be of interest to researchers using the Xiphophorus model. This work also provides an archive for future studies in molecular mechanisms of sexual dimorphism and evolution, and can be used in comparative studies of other fish.

Constructing a fish metabolic network model

We report the construction of a genome-wide fish metabolic network model, MetaFishNet, and its application to analyzing high throughput gene expression data. This model is a stepping stone to broader applications of fish systems biology, for example by guiding study design through comparison with human metabolism and the integration of multiple data types. MetaFishNet resources, including a pathway enrichment analysis tool, are accessible at http://metafishnet.appspot.com.

Melanocytic neoplasms in a black rhinoceros (Diceros bicornis) and an Indian rhinoceros (Rhinoceros unicornis)

Melanocytic neoplasms were diagnosed in a captive black rhinoceros (Diceros bicornis) and a captive Indian rhinoceros (Rhinoceros unicornis) from different facilities. The first case was a 10-yr-old, captive-born male black rhinoceros that presented with a small firm cutaneous mass on the dorsal midline. Aspirate cytology results were suggestive of a melanocytic neoplasm, and histologic examination of the excised mass confirmed a well-differentiated neoplasm with much pigment production, minimal anaplasia, and no mitotic figures. Several months after mass removal, a similar mass with identical histologic features was excised from the right medial thigh. The second case was a 28-yr-old, wild-born female Indian rhinoceros that presented with a draining wound at the coronary band of a rear digit. Histologic examination of a biopsy from this lesion revealed a melanocytic neoplasm with moderate cellular anaplasia, frequent mitoses, and scant pigment production. At necropsy, the tumor was found to ablate P3 and most deep tissues of the toe. No evidence of vascular invasion or metastasis was found. These two cases represent the only melanocytic neoplasms in Rhinoceridae reported in detail in the literature.

Ultraviolet A does not induce melanomas in a Xiphophorus hybrid fish model

We examined the wavelength dependence of ultraviolet (UV) ra-diation (UVR)-induced melanoma in a Xiphophorus backcross hybrid model previously reported to be susceptible to melanoma induction by ultraviolet A (UVA) and visible light. Whereas ultraviolet B (UVB) irradiation of neonates yielded high frequencies of melanomas in pigmented fish, UVA irradiation resulted in melanoma frequencies that were not significantly different from unirradiated fish. Spontaneous and UV-induced melanoma frequencies correlated with the degree of pigmentation as expected from previous studies, and the histopathology phenotypes of the melanomas were not found in significantly different proportions in UV-treated and -untreated tumor-bearing fish. Our results support the conclusion that a brief early-life exposure to UVB radiation causes melanoma formation in this animal model. These data are consistent with an essential role for direct DNA damage, including cyclobutane dimers and (6-4) photoproducts, in the etiology of melanoma.

Fishing for intestinal cancer models: unraveling gastrointestinal homeostasis and tumorigenesis in zebrafish

Zebrafish has proven to be a highly versatile model for comprehensive studies of gene function in development. Given that the molecular pathways involved in epithelial carcinogenesis appear to be conserved across vertebrates, zebrafish is now considered as a valid model to study tumor biology. Development and homeostasis in multicellular organisms are dependent on a complex interplay between cell proliferation, migration, differentiation, and cell death. The Wnt signaling pathway is a major signaling pathway during embryonic development and is the key regulator of self-renewal homeostasis in several adult tissues. A large body of knowledge on adult stem-cell biology has arisen from the study of the intestinal epithelium over the past 20 years. The Wnt pathway has appeared as its principal regulator of homeostatic self-renewal. Moreover, most cancers of the intestine are caused by activating mutations in the Wnt pathway. Recently, zebrafish models have been developed to study Wnt pathway-induced cancer. An appealing avenue for cancer research in zebrafish is large-scale screens to identify chemotherapeutic and chemopreventive agents in conjunction with the in vivo imaging approaches that zebrafish affords.

Genetic and environmental melanoma models in fish

Experimental animal models are extremely valuable for the study of human diseases, especially those with underlying genetic components. The exploitation of various animal models, from fruitflies to mice, has led to major advances in our understanding of the etiologies of many diseases, including cancer. Cutaneous malignant melanoma is a form of cancer for which both environmental insult (i.e., UV) and hereditary predisposition are major causative factors. Fish melanoma models have been used in studies of both spontaneous and induced melanoma formation. Genetic hybrids between platyfish and swordtails, different species of the genus Xiphophorus, have been studied since the 1920s to identify genetic determinants of pigmentation and melanoma formation. Recently, transgenesis has been used to develop zebrafish and medaka models for melanoma research. This review will provide a historical perspective on the use of fish models in melanoma research, and an updated summary of current and prospective studies using these unique experimental systems.

The role of ultraviolet radiation in melanomagenesis

The role of ultraviolet radiation (UV) in the pathogenesis has been discussed controversially for many decades. Studies in mice (SCID, HGF/SF, SV40T) which develop malignant melanoma, show a role of UVB in melanomagenesis. In contrast to this, the role of UVA is less clear. We will review the recent in vitro and in vivo data in support of the hypothesis that UVA is also involved in the development of malignant melanoma. The role of UVA in p53 activation, apoptosis, cell cycle arrest and photoproduct formation is discussed.

Sperm cryopreservation in guppies and black mollies--a generalized freezing protocol for livebearers in Poeciliidae

In this study, we evaluated various parameters of sperm cryopreservation in two livebearers, guppies (Poecilia reticulata) and black mollies (P. latipinna). Our results suggested a common freezing protocol for the guppies and mollies: suspend sperm in Hanks' balanced salt solution (HBSS) at 300 mOsm/kg, use 14% glycerol as cryoprotectant, cool at 25 degrees C/min, and thaw at 40 degrees C in a water bath for 7s. Live young were produced from females inseminated with frozen-thawed sperm in both species. In guppies, percent fertilization (F) and the number of embryos (N) produced with cryopreserved sperm (F=50%, N=74, from 26 females) were similar to those of fresh controls (F=54%, N=61, from 22 females). Interestingly, this same freezing protocol has been used successfully for sperm cryopreservation in green swordtails Xiphophorus helleri, and platyfish of X. couchianus with post-thaw motility as high as 80%. All these species belong to the family of Poeciliidae, and their sperm are similar in morphology exhibiting the absence of acrosome, elongate sperm head, and the long mitochondrial sheaths. Besides their internal fertilization reproduction mode, these fish are also small in size (2-4 cm) and live in a freshwater environment. Sperm cryopreservation in fish has been generally recognized as species specific, and new protocols are required for new species. However, results presented in this study suggested otherwise. Thus, sperm cryopreservation methods optimized for one species may be applicable to others if they are taxonomical closely related species with similar sperm morphology and reproduction mode. Considering the enormous number of fish species on the planet, development of generalized sperm freezing protocols for species in groups could have additional advantages for genetic conservation.

The complete mitochondrial genome of the RR-B strain of swordtail (Xiphophorus helleri)

BACKGROUND AND AIMS

The swordtail (Xiphophorus helleri) has been used in studies of behavior, phylogenetics, genetics, physiology, cell biology, cancer research, and biomedicine. Mitochondrial DNA (mtDNA) studies are of pressing need in order to assess the population history of the species.

MATERIALS AND METHOD

In this study, we present the complete mtDNA genome sequence of two specimens: one from a RR-B strain, a 27-generation inbred line; and one non-selective swordtail with red eyes and red body color from the Guangzhou market, measuring 16,638 and 16,635 bp, respectively.

RESULTS

The genome comprises 13 protein-coding genes, 22 tRNAs, two rRNAs and a major non-coding region. The comparison of the two specimens' mitogenomes revealed a relatively low number (57) of single nucleotide polymorphisms-29 located in protein-coding genes, 11 in rRNA genes, six in tRNA genes, and six in the non-coding region.

CONCLUSION

We present an important genetic resource for the RR-B strain of swordtails and swordtail species in general.

Sperm cryopreservation of a live-bearing fish, Xiphophorus couchianus: male-to-male variation in post-thaw motility and production of F(1) hybrid offspring

Fishes of the genus Xiphophorus are well-studied biomedical research models, and some species, such as X. couchianus, are currently listed as endangered in the wild. Sperm cryopreservation in these live-bearing fishes has begun recently. Thus far, live young have been produced with cryopreserved sperm only in one species (Xiphophorus helleri). In this study, the goal was to develop a practical protocol for sperm cryopreservation of Xiphophorus couchianus, and to produce live young with cryopreserved sperm. Sperm were collected by crushing of testis in Hanks' balanced salt solution at an osmolality of 500 mOsmol/kg (HBSS500), and were cryopreserved with 14% glycerol (v/v) as cryoprotectant at a cooling rate of 20 degrees C/min from 5 to -80 degrees C in 250-microL French straws. For artificial insemination, samples were thawed at 40 degrees C for 5 s in a water bath, washed once using fresh HBSS500 by centrifuging at 1000 g for 5 min at 4 degrees C, concentrated into approximately 5 microL, and injected into virgin females of Xiphophorus maculatus. The inseminated females were monitored for 90 days for subsequent discharge of live young. Results from 2006 and 2007 showed considerable male-to-male variation in post-thaw motility (from 1 to 70%). Offspring were produced by cryopreserved sperm in two tanks (of three) at 36 and 66 days after insemination in 2007. Paternity was confirmed via phenotypes (body color) and genotypes (microsatellite genetic marker) of the hybrid offspring. Overall, a practical protocol for sperm cryopreservation and artificial insemination is provided to preserve X. couchianus, which is an important biomedical research model, and also currently listed as an endangered species in the International Union for Conservation of Nature (IUCN) red list.

Current status of sperm cryopreservation in biomedical research fish models: zebrafish, medaka, and Xiphophorus

Aquarium fishes are becoming increasingly important because of their value in biomedical research and the ornamental fish trade, and because many have become threatened or endangered in the wild. This review summarizes the current status of sperm cryopreservation in three fishes widely used in biomedical research: zebrafish, medaka, and live-bearing fishes of the genus Xiphophorus, and will focus on the needs and opportunities for future research and application of cryopreservation in aquarium fish. First, we summarize the basic biological characteristics regarding natural habitat, testis structure, spermatogenesis, sperm morphology, and sperm physiology. Second, we compare protocol development of sperm cryopreservation. Third, we emphasize the importance of artificial fertilization in sperm cryopreservation to evaluate the viability of thawed sperm. We conclude with a look to future research directions for sperm cryopreservation and the application of this technique in aquarium species.