Comparative Analysis of the Testis and Ovary Transcriptomes in Zebrafish by Combining Experimental and Computational Tools

Studies on the zebrafish model have contributed to our understanding of several important developmental processes, especially those that can be easily studied in the embryo. However, our knowledge on late events such as gonad differentiation in the zebrafish is still limited. Here we provide an analysis on the gene sets expressed in the adult zebrafish testis and ovary in an attempt to identify genes with potential role in (zebra)fish gonad development and function. We produced 10 533 expressed sequence tags (ESTs) from zebrafish testis or ovary and downloaded an additional 23 642 gonad-derived sequences from the zebrafish EST database. We clustered these sequences together with over 13 000 kidney-derived zebrafish ESTs to study partial transcriptomes for these three organs. We searched for genes with gonad-specific expression by screening macroarrays containing at least 2600 unique cDNA inserts with testis-, ovary- and kidney-derived cDNA probes. Clones hybridizing to only one of the two gonad probes were selected, and subsequently screened with computational tools to identify 72 genes with potentially testis-specific and 97 genes with potentially ovary-specific expression, respectively. PCR-amplification confirmed gonad-specificity for 21 of the 45 clones tested (all without known function). Our study, which involves over 47 000 EST sequences and specialized cDNA arrays, is the first analysis of adult organ transcriptomes of zebrafish at such a scale. The study of genes expressed in adult zebrafish testis and ovary will provide useful information on regulation of gene expression in teleost gonads and might also contribute to our understanding of the development and differentiation of reproductive organs in vertebrates.

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N-Cadherin Is Critical for the Survival of Germ Cells, the Formation of Steroidogenic Cells, and the Architecture of Developing Mouse Gonads

Cells ◽

10.3390/cells8121610 ◽

2019 ◽

Vol 8 (12) ◽

pp. 1610 ◽

Cited By ~ 2

Author(s):

Rafal P. Piprek ◽

Michal Kolasa ◽

Dagmara Podkowa ◽

Malgorzata Kloc ◽

Jacek Z. Kubiak

Keyword(s):

Germ Cells ◽

Hormonal Regulation ◽

Critical Role ◽

Somatic Cells ◽

Gonad Development ◽

Knock Out ◽

Gonad Differentiation ◽

Steroidogenic Cells ◽

The Individual ◽

And Function

Normal gonad development assures the fertility of the individual. The properly functioning gonads must contain a sufficient number of the viable germ cells, possess a correct architecture and tissue structure, and assure the proper hormonal regulation. This is achieved by the interplay between the germ cells and different types of somatic cells. N-cadherin coded by the Cdh2 gene plays a critical role in this interplay. To gain an insight into the role of N-cadherin in the development of mouse gonads, we used the Cre-loxP system to knock out N-cadherin separately in two cell lines: the SF1+ somatic cells and the OCT4+ germ cells. We observed that N-cadherin plays a key role in the survival of both female and male germ cells. However, the N-cadherin is not necessary for the differentiation of the Sertoli cells or the initiation of the formation of testis cords or ovigerous cords. In the later stages of gonad development, N-cadherin is important for the maintenance of testis cord structure and is required for the formation of steroidogenic cells. In the ovaries, N-cadherin is necessary for the formation of the ovarian follicles. These results indicate that N-cadherin plays a major role in gonad differentiation, structuralization, and function.

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Long non-coding RNAs in wild wheat progenitors

10.1101/301804 ◽

2018 ◽

Author(s):

Alice Pieri ◽

Mario Enrico Pè ◽

Edoardo Bertolini

Keyword(s):

Aegilops Tauschii ◽

Noncoding Rnas ◽

Reproductive Organs ◽

Long Noncoding Rnas ◽

D Genome ◽

Specific Expression ◽

Wild Wheat ◽

Organ Specific ◽

Species Specific ◽

And Function

AbstractTriticum urartu and Aegilops tauschii are the diploid progenitors of the hexaploid Triticum aestivum (AuAuBBDD), donors of the Au and D genome respectively. In this work we investigate the long noncoding RNAs (lncRNAs) component of the genomes of these two wild wheat relatives. Sixty-eight RNA-seq libraries generated from several organs and conditions were retrieved from public databases. We annotated and characterized 14,515 T. urartu and 20,908 Ae. tauschii bona-fide lncRNA transcripts that show features similar to those of other plant and animal counterparts. Thousands of lncRNAs were found significantly modulated in different organs and exhibited organ specific expression, with a predominant accumulation in the spike, fostering the hypothesis of their crucial role in reproductive organs. Most of the organ-specific lncRNAs were found associated with transposable elements (TEs), indicating the possible role of TEs in lncRNA origin, differentiation and function. The majority of T. urartu and Ae. tauschii lncRNAs appear to be species-specific; nevertheless, we found some lncRNAs conserved between the two wheat progenitors, highlighting the presence and conservation of exonic splicing enhancers sites in multi-exon conserved lncRNAs. In addition, we found cases of lncRNA conservation and their cis regulatory regions spanning the wheat pre-domestication and post-domestication period. Altogether, these results represent the first comprehensive genome-wide encyclopedia of lncRNAs in wild wheat relatives, and they provide clues as to the hidden regulatory pathway mediated by long noncoding RNAs in these largely unexplored wheat progenitors.

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Runx transcription factors in the development and function of the definitive hematopoietic system

Blood ◽

10.1182/blood-2016-12-689109 ◽

2017 ◽

Vol 129 (15) ◽

pp. 2061-2069 ◽

Cited By ~ 44

Author(s):

Marella de Bruijn ◽

Elaine Dzierzak

Keyword(s):

Transcription Factors ◽

Current Knowledge ◽

Biological Effects ◽

Regulation Of Gene Expression ◽

Loss Of Function ◽

Specific Expression ◽

Hematopoietic Stem ◽

Hematopoietic Development ◽

Cell Lineages ◽

And Function

AbstractThe Runx family of transcription factors (Runx1, Runx2, and Runx3) are highly conserved and encode proteins involved in a variety of cell lineages, including blood and blood-related cell lineages, during developmental and adult stages of life. They perform activation and repressive functions in the regulation of gene expression. The requirement for Runx1 in the normal hematopoietic development and its dysregulation through chromosomal translocations and loss-of-function mutations as found in acute myeloid leukemias highlight the importance of this transcription factor in the healthy blood system. Whereas another review will focus on the role of Runx factors in leukemias, this review will provide an overview of the normal regulation and function of Runx factors in hematopoiesis and focus particularly on the biological effects of Runx1 in the generation of hematopoietic stem cells. We will present the current knowledge of the structure and regulatory features directing lineage-specific expression of Runx genes, the models of embryonic and adult hematopoietic development that provide information on their function, and some of the mechanisms by which they affect hematopoietic function.

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Embryonic exposure to 10 μg L−1lead results in female-specific expression changes in genes associated with nervous system development and function and Alzheimer's disease in aged adult zebrafish brain

Metallomics ◽

10.1039/c5mt00267b ◽

2016 ◽

Vol 8 (6) ◽

pp. 589-596 ◽

Cited By ~ 16

Author(s):

Jinyoung Lee ◽

Jennifer L. Freeman

Keyword(s):

System Development ◽

Expression Patterns ◽

Global Gene Expression ◽

Nervous System Development ◽

Adult Zebrafish ◽

Specific Expression ◽

Embryonic Exposure ◽

Specific Manner ◽

And Function ◽

Female Specific

Embryonic exposure to Pb at levels as low as 10 μg L−1disturb global gene expression patterns in a sex-specific manner.

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Spring Freeze Damage of Pecan Bloom: A Review

Horticulturae ◽

10.3390/horticulturae6040082 ◽

2020 ◽

Vol 6 (4) ◽

pp. 82

Author(s):

Amandeep Kaur ◽

Louise Ferguson ◽

Niels Maness ◽

Becky Carroll ◽

William Reid ◽

...

Keyword(s):

Tree Height ◽

The United States ◽

Reproductive Organs ◽

Tree Age ◽

The Us ◽

Nut Production ◽

Freeze Damage ◽

Terminal Buds ◽

And Function ◽

The Impact

Pecan is native to the United States. The US is the world’s largest pecan producer with an average yearly production of 250 to 300 million pounds; 80 percent of the world’s supply. Georgia, New Mexico, Texas, Arizona, Oklahoma, California, Louisiana, and Florida are the major US pecan producing states. Pecan trees frequently suffer from spring freeze at bud break and bloom as the buds are quite sensitive to freeze damage. This leads to poor flower and nut production. This review focuses on the impact of spring freeze during bud differentiation and flower development. Spring freeze kills the primary terminal buds, the pecan tree has a second chance for growth and flowering through secondary buds. Unfortunately, secondary buds have less bloom potential than primary buds and nut yield is reduced. Spring freeze damage depends on severity of the freeze, bud growth stage, cultivar type and tree age, tree height and tree vigor. This review discusses the impact of temperature on structure and function of male and female reproductive organs. It also summarizes carbohydrate relations as another factor that may play an important role in spring growth and transition of primary and secondary buds to flowers.

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Comparative effects of Orchis anatolica vs. the red Korean Panax ginseng treatments on testicular structure and function of adult male mice

Journal of Complementary and Integrative Medicine ◽

10.1515/jcim-2012-0035 ◽

2015 ◽

Vol 12 (1) ◽

Author(s):

Nabil A. Khouri ◽

Haytham M. Daradka ◽

Mohammed Z. Allouh ◽

Ahmad S. Alkofahi

Keyword(s):

Panax Ginseng ◽

Male Fertility ◽

Virgin Female ◽

Reproductive Organs ◽

Serum Markers ◽

Structure And Function ◽

Control Group ◽

Male Mice ◽

Fertility Potential ◽

And Function

Abstract: The effects of: Both plants were administered orally to two separate mice groups at a dose of 800 mg/kg/day for 35 days and compared with control group. After treatment, 5 mice of each group were sacrificed and total mice weights, reproductive organs’ weights, spermatogenesis, and androgenic serum markers were investigated. The remaining mice from all groups were allowed to mate with virgin female mice to explore male fertility potential.: Results indicated that body and organs’ weights were increased significantly in mice treated with: We can conclude that

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Modulation of Innate Immune Toxicity by Silver Nanoparticle Exposure and the Preventive Effects of Pterostilbene

International Journal of Molecular Sciences ◽

10.3390/ijms22052536 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2536

Author(s):

Rong-Jane Chen ◽

Chiao-Ching Huang ◽

Rosita Pranata ◽

Yu-Hsuan Lee ◽

Yu-Ying Chen ◽

...

Keyword(s):

Silver Nanoparticles ◽

Good Alternative ◽

Innate Immune ◽

Toxic Effects ◽

Transgenic Zebrafish ◽

Zebrafish Model ◽

Cytokines And Chemokines ◽

Living Organisms ◽

And Function ◽

Immune Toxicity

Silver nanoparticles pose a potential risk to ecosystems and living organisms due to their widespread use in various fields and subsequent gradual release into the environment. Only a few studies have investigated the effects of silver nanoparticles (AgNPs) toxicity on immunological functions. Furthermore, these toxic effects have not been fully explored. Recent studies have indicated that zebrafish are considered a good alternative model for testing toxicity and for evaluating immunological toxicity. Therefore, the purpose of this study was to investigate the toxicity effects of AgNPs on innate immunity using a zebrafish model and to investigate whether the natural compound pterostilbene (PTE) could provide protection against AgNPs-induced immunotoxicity. Wild type and neutrophil- and macrophage-transgenic zebrafish lines were used in the experiments. The results indicated that the exposure to AgNPs induced toxic effects including death, malformation and the innate immune toxicity of zebrafish. In addition, AgNPs affect the number and function of neutrophils and macrophages. The expression of immune-related cytokines and chemokines was also affected. Notably, the addition of PTE could activate immune cells and promote their accumulation in injured areas in zebrafish, thereby reducing the damage caused by AgNPs. In conclusion, AgNPs may induce innate immune toxicity and PTE could ameliorate this toxicity.

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Involvement of Thyroid Hormones in Brain Development and Cancer

Cancers ◽

10.3390/cancers13112693 ◽

2021 ◽

Vol 13 (11) ◽

pp. 2693

Author(s):

Gabriella Schiera ◽

Carlo Maria Di Liegro ◽

Italia Di Liegro

Keyword(s):

Nervous System ◽

Thyroid Hormones ◽

Brain Development ◽

Placental Transfer ◽

Regulation Of Gene Expression ◽

Mammalian Brain ◽

Cancer Proliferation ◽

Fetal Thyroid ◽

Genomic Effects ◽

And Function

The development and maturation of the mammalian brain are regulated by thyroid hormones (THs). Both hypothyroidism and hyperthyroidism cause serious anomalies in the organization and function of the nervous system. Most importantly, brain development is sensitive to TH supply well before the onset of the fetal thyroid function, and thus depends on the trans-placental transfer of maternal THs during pregnancy. Although the mechanism of action of THs mainly involves direct regulation of gene expression (genomic effects), mediated by nuclear receptors (THRs), it is now clear that THs can elicit cell responses also by binding to plasma membrane sites (non-genomic effects). Genomic and non-genomic effects of THs cooperate in modeling chromatin organization and function, thus controlling proliferation, maturation, and metabolism of the nervous system. However, the complex interplay of THs with their targets has also been suggested to impact cancer proliferation as well as metastatic processes. Herein, after discussing the general mechanisms of action of THs and their physiological effects on the nervous system, we will summarize a collection of data showing that thyroid hormone levels might influence cancer proliferation and invasion.

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Function of Circular RNAs in Fish and Their Potential Application as Biomarkers

International Journal of Molecular Sciences ◽

10.3390/ijms22137119 ◽

2021 ◽

Vol 22 (13) ◽

pp. 7119

Author(s):

Golam Rbbani ◽

Artem Nedoluzhko ◽

Jorge Galindo-Villegas ◽

Jorge M. O. Fernandes

Keyword(s):

Growth Regulation ◽

Functional Characterization ◽

Circular Rnas ◽

Farmed Fish ◽

Developmentally Regulated ◽

Specific Expression ◽

Cell Type Specific Expression ◽

Cell Type Specific ◽

Taxonomic Groups ◽

And Function

Circular RNAs (circRNAs) are an emerging class of regulatory RNAs with a covalently closed-loop structure formed during pre-mRNA splicing. Recent advances in high-throughput RNA sequencing and circRNA-specific computational tools have driven the development of novel approaches to their identification and functional characterization. CircRNAs are stable, developmentally regulated, and show tissue- and cell-type-specific expression across different taxonomic groups. They play a crucial role in regulating various biological processes at post-transcriptional and translational levels. However, the involvement of circRNAs in fish immunity has only recently been recognized. There is also broad evidence in mammals that the timely expression of circRNAs in muscle plays an essential role in growth regulation but our understanding of their expression and function in teleosts is still very limited. Here, we discuss the available knowledge about circRNAs and their role in growth and immunity in vertebrates from a comparative perspective, with emphasis on cultured teleost fish. We expect that the interest in teleost circRNAs will increase substantially soon, and we propose that they may be used as biomarkers for selective breeding of farmed fish, thus contributing to the sustainability of the aquaculture sector.

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