Translate this page to:
In JoVE (2)
- RNA Isolation from Embryonic Zebrafish and cDNA Synthesis for Gene Expression Analysis
- Global Gene Expression Analysis Using a Zebrafish Oligonucleotide Microarray Platform
Other Publications (18)
- Diabetes Technology & Therapeutics
- The Journal of Experimental Biology
- Environmental Toxicology and Chemistry / SETAC
- Aquatic Toxicology (Amsterdam, Netherlands)
- Environmental Toxicology
- Genome Research
- Genes & Development
- BMC Genomics
- Journal of Immunotherapy (Hagerstown, Md. : 1997)
- Genes, Chromosomes & Cancer
- Environmental Health Perspectives
- Neurotoxicology and Teratology
- Methods in Cell Biology
- Proceedings of the National Academy of Sciences of the United States of America
Articles by Jennifer L. Freeman in JoVE
RNA Isolation from Embryonic Zebrafish and cDNA Synthesis for Gene Expression Analysis
Samuel M. Peterson, Jennifer L. Freeman
School of Health Sciences, Purdue University
The isolation of high quality, intact RNA is an essential step in many laboratory protocols. Here, we demonstrate RNA extraction from whole zebrafish embryos and cDNA synthesis for subsequent application in various experimental procedures including gene expression microarray analysis.
Global Gene Expression Analysis Using a Zebrafish Oligonucleotide Microarray Platform
Samuel M. Peterson, Jennifer L. Freeman
School of Health Sciences, Purdue University
Gene microarrays are powerful tools in gene expression profiling at a genome-wide level. This technology has application in a variety of biological disciplines including developmental biology and toxicology. In this video, we detail a protocol for global gene expression analysis using a comprehensive oligonucleotide microarray platform for the zebrafish.
Other articles by Jennifer L. Freeman on PubMed
Beta 2-adrenergic Receptor Stimulated, G Protein-coupled Receptor Kinase 2 Mediated, Phosphorylation of Ribosomal Protein P2
Biochemistry. Oct, 2002 | Pubmed ID: 12379128
G protein-coupled receptor kinases are well characterized for their ability to phosphorylate and desensitize G protein-coupled receptors (GPCRs). In addition to phosphorylating the beta2-adrenergic receptor (beta2AR) and other receptors, G protein-coupled receptor kinase 2 (GRK2) can also phosphorylate tubulin, a nonreceptor substrate. To identify novel nonreceptor substrates of GRK2, we used two-dimensional gel electrophoresis to find cellular proteins that were phosphorylated upon agonist-stimulation of the beta2AR in a GRK2-dependent manner. The ribosomal protein P2 was identified as an endogenous HEK-293 cell protein whose phosphorylation was increased following agonist stimulation of the beta2AR under conditions where tyrosine kinases, PKC and PKA, were inhibited. P2 along with its other family members, P0 and P1, constitutes a part of the elongation factor-binding site connected to the GTPase center in the 60S ribosomal subunit. Phosphorylation of P2 is known to regulate protein synthesis in vitro. Further, P2 and P1 are shown to be good in vitro substrates for GRK2 with K(M) values approximating 1 microM. The phosphorylation sites in GRK2-phosphorylated P2 are identified (S102 and S105) and are identical to the sites known to regulate P2 activity. When the 60S subunit deprived of endogenous P1 and P2 is reconstituted with GRK2-phosphorylated P2 and unphosphorylated P1, translational activity is greatly enhanced. These findings suggest a previously unrecognized relationship between GPCR activation and the translational control of gene expression mediated by GRK2 activation and P2 phosphorylation and represent a potential novel signaling pathway responsible for P2 phosphorylation in mammals.
Diabetes Technology & Therapeutics. 2003 | Pubmed ID: 12828817
1,5-Anhydroglucitol (1,5-AG), the 1-deoxy form of glucose, has been measured and used clinically in Japan for over a decade to monitor short-term glycemic control. Evaluation of glucose control otherwise requires measuring plasma glucose or glycated proteins whose levels reflect average glucose concentration over the half-life of the protein analyzed. Hemoglobin A1c measurements reflect blood glucose levels over that past 2-3 months, while fructosamine can be used to evaluate glycemic control over 10-14 days. In contrast, 1,5-AG levels in blood respond within 24 h as a result of glucose's competitive inhibition of 1,5-AG reabsorption in the kidney tubule. When glucose levels rise, even transiently, urinary loss of 1,5-AG occurs, and circulating levels fall. Because of changes in renal hemodynamics in normal pregnancies, 1,5-AG appears of limited usefulness in evaluation of gestational diabetes. However, the characteristics of 1,5-AG levels in patients with moderate to near-normal glycemic control suggest that it may be a valuable complement to frequent self-monitoring or continuous monitoring of plasma glucose to confirm stable glycemic control. Measurements performed daily or weekly in a given patient would suggest that overall glycemic control has been stable or improved if 1,5-AG levels are stable or increasing. If 1,5-AG levels fall, greater attention to glucose monitoring and both lifestyle and medical management could be prescribed to correct the glycemic excursions that would underlie such changes. The behavior of this analyte is different from all others used in the management of diabetes, creating potential opportunities for its use in clinical practice.
The Journal of Experimental Biology. Dec, 2004 | Pubmed ID: 15557032
Amphibian metamorphosis is a complex process that has been speculated to involve DNA amplification and chromatin rearrangement. While recent studies have concentrated on chromatin rearrangement, only a few studies have dealt with variation in the amount of DNA during amphibian metamorphosis. In this study, nuclei were isolated from Xenopus laevis at various developmental stages. The nuclei were examined in both an unfixed state and a fixed state. The nuclei were stained with propidium iodide and analyzed by flow cytometry to determine their fluorescence intensity. The unfixed nuclei had higher fluorescence variation compared with the fixed nuclei. This increase in variation appeared due to the presence of nuclei of variable fluorescence intensity within the unfixed nuclei. Upon optimum fixation, which has been speculated to result in more homogeneous chromatin conformation and to reduce staining artifacts, the nuclei were observed to have less fluorescence intensity variation. The differential fluorescence observed in this study is consistent with the hypothesis that large-scale intra-individual DNA variation is not associated with amphibian metamorphosis.
Developmental Impact of Atrazine on Metamorphing Xenopus Laevis As Revealed by Nuclear Analysis and Morphology
Environmental Toxicology and Chemistry / SETAC. Jul, 2005 | Pubmed ID: 16050581
Atrazine is one of the major surface water contaminants in the midwestern United States. Speculations have arisen on the potential effects of atrazine contamination to anuran larvae developing in these surface waters. In this study, Xenopus laevis tadpoles were exposed to environmentally relevant concentrations of atrazine. Nuclear and morphological endpoints were used to assess the effects of atrazine on developing X. laevis. Atrazine significantly affected metamorphing X. laevis after three-weeks exposure compared to controls as revealed by flow cytometric nuclear DNA analysis. The flow cytometric analysis was reflective of developmental effects. The number of nuclei per organism also was analyzed. Nuclei number was found to be associated with X. laevis development. Nuclei counting showed significant effects of atrazine after five-weeks exposure. A third endpoint, Nieuwkoop and Faber (NF) morphological staging, also demonstrated that atrazine significantly affected development after four weeks. Atrazine was found to alter the timing of metamorphosis of X. laevis using both nuclear analysis and gross morphology. The NF staging was found to be a sensitive assay to measure effects of development, whereas flow cytometry provided an impartial quantitative measure.
Differential Metamorphosis Alters the Endocrine Response in Anuran Larvae Exposed to T3 and Atrazine
Aquatic Toxicology (Amsterdam, Netherlands). Nov, 2005 | Pubmed ID: 16213604
Pesticide chemical contamination is one of the suspected contributors of the amphibian population decline. The herbicide atrazine is one of the major surface water contaminants in the U.S. A previous study has shown that atrazine at concentrations as low as 100 parts per billion (ppb) increased the time to metamorphosis in Xenopus laevis tadpoles. However, questions remain as to the applicability of a study of a non-native species to a native organism. The possible effects of atrazine on developing Bufo americanus were explored. Atrazine at potentially (albeit high) environmental concentrations was found not to delay the metamorphosis of developing B. americanus tadpoles as observed in X. laevis. Several studies have indicated that atrazine affects thyroid hormones. Since thyroid hormones are critical in amphibian metamorphosis, B. americanus and X. laevis tadpoles were exposed to exogenous 3,5,3'-triiodothyronine (T3). X. laevis were found to be more responsive to the effects of exogenous T3 compared to B. americanus, indicating that X. laevis may be more sensitive to endocrine active chemicals than B. americanus. In X. laevis, nuclear heterogeneity has been associated with metamorphosis. Flow cytometric analysis of the nuclei of normal metamorphing B. americanus indicates a decrease in the amount of thyroid mediated chromatin alterations relative to the nuclei of metamorphing X. laevis. Indications are that the differential response to endocrine disruption is due to the differential role of chromatin associated gene expression during metamorphosis of B. americanus versus X. laevis. A second native species, Hyla versicolor, was observed to have the X. laevis nuclear pattern with respect to metamorphosis. As such, sensitivity to endocrine disruption is hypothesized not to be limited to laboratory non-native species.
Environmental Toxicology. Jun, 2006 | Pubmed ID: 16646021
Concerns have arisen about the possible effects of herbicide contamination in aquatic ecosystems. Crop herbicides are introduced into the aquatic environment both inadvertently through runoff events and intentionally through the use of those registered for use in waterways. Acetochlor and atrazine are two agricultural crop herbicides that have often been reported to contaminate waters. Diquat and fluridone are both registered aquatic management herbicides. In this study, a mammalian in vitro cell cytotoxicity assay was used to evaluate the cytotoxicity of these four commonly used herbicides. The ranked order of the cytotoxicity was: diquat (C(1/2) = 0.036 mM +/- 0.011) > acetochlor (C(1/2) = 0.060 mM +/- 0.010) > fluridone (C(1/2) = 0.172 mM +/- 0.029) atrazine (C(1/2) = 0.581 mM +/- 0.050). In addition, flow cytometric analysis was conducted on CHO cells to investigate the potential impact of these four herbicides on the cell cycle. Acetochlor and diquat had the greatest impact on the cell cycle. Acetochor exposure resulted in a decreased number of cells in the G1 phase of the cell cycle, whereas diquat exposure resulted in a decreased number of cells in both the G1 and G2 phases. Both atrazine and fluridone resulted in a decrease in cells in the G2 phase. The agricultural crop herbicides and aquatic management herbicides gave similar results in cytotoxicity and in the cell-cycle assay at the end points tested.
Genome Research. Aug, 2006 | Pubmed ID: 16809666
DNA copy number variation has long been associated with specific chromosomal rearrangements and genomic disorders, but its ubiquity in mammalian genomes was not fully realized until recently. Although our understanding of the extent of this variation is still developing, it seems likely that, at least in humans, copy number variants (CNVs) account for a substantial amount of genetic variation. Since many CNVs include genes that result in differential levels of gene expression, CNVs may account for a significant proportion of normal phenotypic variation. Current efforts are directed toward a more comprehensive cataloging and characterization of CNVs that will provide the basis for determining how genomic diversity impacts biological function, evolution, and common human diseases.
Nature. Nov, 2006 | Pubmed ID: 17122850
Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies.
Genes & Development. Jan, 2007 | Pubmed ID: 17210788
Proper chromosome segregation is essential for maintenance of genomic integrity and instability resulting from failure of this process may contribute to cancer. Here, we demonstrate that a mutation in the mitotic regulator separase is responsible for the cell cycle defects seen in the zebrafish mutant, cease&desist (cds). Analysis of cds homozygous mutant embryos reveals high levels of polyploidy and aneuploidy, spindle defects, and a mitotic exit delay. Carcinogenesis studies demonstrated that cds heterozygous adults have a shift in tumor spectrum with an eightfold increase in the percentage of fish bearing epithelial tumors, indicating that separase is a tumor suppressor gene in vertebrates. These data strongly support a conserved cross-species role for mitotic checkpoint genes in genetic stability and epithelial carcinogenesis.
BMC Genomics. 2007 | Pubmed ID: 17597531
The zebrafish (Danio rerio) is an important vertebrate model organism system for biomedical research. The syntenic conservation between the zebrafish and human genome allows one to investigate the function of human genes using the zebrafish model. To facilitate analysis of the zebrafish genome, genetic maps have been constructed and sequence annotation of a reference zebrafish genome is ongoing. However, the duplicative nature of teleost genomes, including the zebrafish, complicates accurate assembly and annotation of a representative genome sequence. Cytogenetic approaches provide "anchors" that can be integrated with accumulating genomic data.
CMRF-56 Immunoselected Blood Dendritic Cell Preparations Activated with GM-CSF Induce Potent Antimyeloma Cytotoxic T-cell Responses
Journal of Immunotherapy (Hagerstown, Md. : 1997). Oct, 2007 | Pubmed ID: 17893566
The efficient antigen-presenting function of dendritic cells (DC) makes them an attractive cellular adjuvant for clinical immunotherapeutic protocols aimed at eradicating minimal residual disease after conventional treatment of multiple myeloma (MM) and other malignancies. We used single-step positive immunoselection with biotinylated CMRF-56 monoclonal antibody to generate a CD11c blood DC (BDC) enriched antigen-presenting cell population, which, after exposure to activation stimuli for as little as 2 hours, displayed a mature costimulatory BDC phenotype and secreted inflammatory cytokines. Of the activation stimuli tested, granulocyte macrophage colony-stimulating factor (GM-CSF) provided optimal activation of the CMRF-56 immunoselected preparations and primed efficient cytotoxic T cell (CTL) responses using MART-1 peptide as a model tumor-associated antigen. In addition, GM-CSF activated CMRF-56 immunoselected cells cross-presented MM cell lysate and improved the MM-specific polyclonal CTL response (no activation 18.8%+/-4.3% vs. GM-CSF activation 40.9%+/-7.3%, P=0.051). CMRF-56 immunoselected BDC migrated in vitro both spontaneously and specifically toward the secondary lymphoid chemokine CCL21. Their migration was also significantly improved by GM-CSF and prostaglandin E2 activation and a greater percentage of activated BDC migrated specifically compared with monocyte-derived DC. These results indicate that the CMRF-56 immunoselected BDC preparations can cross-present antigen for effective anti-MM CTL responses and that limited exposure to maturation stimuli can produce phenotypically and functionally mature migrating DC. CMRF-56 immunoselected cells are suitable for use as part of an immunotherapeutic anti-MM vaccine.
Immunogenetics. May, 2008 | Pubmed ID: 18330557
Novel immune-type receptors (NITRs) are immunoglobulin-variable (V) domain-containing cell surface proteins that possess characteristic activating/inhibitory signaling motifs and are expressed in hematopoietic cells. NITRs are encoded by multigene families and have been identified in bony fish species. A single gene cluster, which encodes 36 NITRs that can be classified into 12 families, has been mapped to zebrafish chromosome 7. We report herein the presence of a second NITR gene cluster on zebrafish chromosome 14, which is comprised of three genes (nitr13, nitr14a, and nitr14b) representing two additional NITR gene families. Phylogenetic analyses indicate that the V domains encoded by the nitr13 and nitr14 genes are more similar to each other than any other zebrafish NITR suggesting that these genes arose from a tandem gene duplication event. Similar analyses comparing zebrafish Nitr13 and Nitr14 to NITRs from other fish species indicate that the nitr13 and nitr14 genes are phylogenetically related to the catfish IpNITR13 and IpNITR15 genes. Sequence features of the chromosomal region encoding nitr13 suggest that this gene arose via retrotransposition.
Genes, Chromosomes & Cancer. Feb, 2009 | Pubmed ID: 18973135
The zebrafish is emerging as a prominent model system for studying the genetics of human development and disease. Genetic alterations that underlie each mutant model can exist in the form of single base changes, balanced chromosomal rearrangements, or genetic imbalances. To detect genetic imbalances in an unbiased genome-wide fashion, array comparative genomic hybridization (CGH) can be used. We have developed a 5-Mb resolution array CGH platform specifically for the zebrafish. This platform contains 286 bacterial artificial chromosome (BAC) clones, enriched for orthologous sequences of human oncogenes and tumor suppressor genes. Each BAC clone has been end-sequenced and cytogenetically assigned to a specific location within the zebrafish genome, allowing for ease of integration of array CGH data with the current version of the genome assembly. This platform has been applied to three zebrafish cancer models. Significant genomic imbalances were detected in each model, identifying different regions that may potentially play a role in tumorigenesis. Hence, this platform should be a useful resource for genetic dissection of additional zebrafish developmental and disease models as well as a benchmark for future array CGH platform development.
Zebrafish. Dec, 2009 | Pubmed ID: 19916830
The zebrafish system has been established as a useful model for the study of carcinogenesis. The cytogenetic characterization of the genome is vital for furthering our understanding of the progression of the disease. Establishing a basic description of the zebrafish chromosomal karyotype and markers for each specific chromosome permitted the first cytogenetic characterization of the reference genome and the genome of cancer models. As the field of cancer cytogenetics is highly dependent on technology, each advance in technique and methodology has resulted in a corresponding wave of discoveries. We have witnessed great improvement in the resolution of the assays allowing for more detailed characterization of cytogenetic abnormalities, including the efficient and accurate identification of DNA copy number alterations of specific chromosomal regions. Herein, we will discuss major advancements in the field of cytogenetics, along with examples of how these technologies have been utilized in studies to characterize zebrafish cancer disease models. Finally, we will discuss the current state of the field and how microarray technology are being implemented to scan the whole genome at high resolution for DNA copy number alterations observed in various cancer types throughout the progression of the disease.
Global Gene Expression Analysis Reveals Dynamic and Developmental Stage-dependent Enrichment of Lead-induced Neurological Gene Alterations
Environmental Health Perspectives. May, 2011 | Pubmed ID: 21147602
The underlying genetic mechanisms specific to subtle neurological alterations associated with environmental lead (Pb) exposures have not been clearly elucidated.
Decreased Axonal Density and Altered Expression Profiles of Axonal Guidance Genes Underlying Lead (Pb) Neurodevelopmental Toxicity at Early Embryonic Stages in the Zebrafish
Neurotoxicology and Teratology. Nov, 2011 | Pubmed ID: 21839828
Previous studies have reported that environmental lead (Pb) exposure can result in neurological alterations in children leading to reduced IQ, attention deficit hyperactivity disorder, and diminished reading and learning abilities. However, the specific alterations in neurodevelopmental morphology and the underlying genetic mechanisms of these alterations have not yet been thoroughly defined. To investigate alterations in neurologic morphology and test the hypothesis that developmental Pb neurotoxicity is partially mediated through alterations in neuronal growth and transport function of axons, the changes of specific axon tracts in the embryonic zebrafish brain were observed with anti-acetylated α-tubulin staining at several developmental time points through 36hours post fertilization (hpf). In addition, the role of a subset of axonogenesis-related genes including shha, epha4b, netrin1b, netrin2, and noiwas investigated with real-time quantitative PCR (qPCR). Pb treatment resulted in decreased axonal density at 18, 20, and 24hpf for specific axon tracts in the midbrain and forebrain. These observations corresponded to an observed down-regulation of shha and epha4b at 14 and 16hpf, respectively. The axonal density in Pb exposed individuals at later stages (30 and 36hpf) was not significantly different from controls. An overexpression of netrin2 at these two developmental stages suggests a novel role for this gene in regulating axonal density specific to Pb neurotoxicity. Although no significant differences in axonal density was observed in the two later developmental stages, further studies are needed to determine if the morphologic alterations observed at the earlier stages will have lasting functional impacts.
Molecular Cytogenetic Methodologies and a BAC Probe Panel Resource for Genomic Analyses in the Zebrafish
Methods in Cell Biology. 2011 | Pubmed ID: 21924167
Molecular cytogenetics is a field that emerged in the 1980s, based on a technique referred to as fluorescence in situ hybridization, (FISH). Using FISH methodologies, a specific DNA sequence or collection of DNA fragments may be selectively labeled with a hapten molecule or fluorescent dye and hybridized to denatured chromosomes, interphase cells, or even chromatin fibers. DNA hybridization kinetics permit these labeled probes to anneal to their complementary sequences on such chromosomal DNA preparations allowing for direct visualization of the sequence of interest in the genome being interrogated. If present, the relative chromosomal position of the sequence can sometimes also be ascertained. Progress in molecular cytogenetic research has advanced the genetic characterization of zebrafish models of human diseases as well as assisted with accurate annotation of the zebrafish reference genome by anchoring large DNA fragments to specific chromosome regions. Using the procedures described in this chapter, hundreds of ambiguous zebrafish bacterial artificial chromosome (BAC) clones have already been assigned to individual genetic linkage groups. Molecular cytogenetic techniques can also be used to study gene duplication events and study the molecular mechanisms by which they arise. Moreover, the availability of a new molecular cytogenetic technique, array-based comparative genomic hybridization (aCGH), is now able to identify gains and losses of DNA segments in zebrafish DNA samples in a genome-wide manner and in a single assay.
Extensive Genetic Diversity and Substructuring Among Zebrafish Strains Revealed Through Copy Number Variant Analysis
Proceedings of the National Academy of Sciences of the United States of America. Jan, 2012 | Pubmed ID: 22203992
Copy number variants (CNVs) represent a substantial source of genomic variation in vertebrates and have been associated with numerous human diseases. Despite this, the extent of CNVs in the zebrafish, an important model for human disease, remains unknown. Using 80 zebrafish genomes, representing three commonly used laboratory strains and one native population, we constructed a genome-wide, high-resolution CNV map for the zebrafish comprising 6,080 CNV elements and encompassing 14.6% of the zebrafish reference genome. This amount of copy number variation is four times that previously observed in other vertebrates, including humans. Moreover, 69% of the CNV elements exhibited strain specificity, with the highest number observed for Tubingen. This variation likely arose, in part, from Tubingen's large founding size and composite population origin. Additional population genetic studies also provided important insight into the origins and substructure of these commonly used laboratory strains. This extensive variation among and within zebrafish strains may have functional effects that impact phenotype and, if not properly addressed, such extensive levels of germ-line variation and population substructure in this commonly used model organism can potentially confound studies intended for translation to human diseases.