scholarly journals Domestication and Temperature Modulate Gene Expression Signatures and Growth in the Australasian Snapper Chrysophrys Auratus

2018 ◽  
Author(s):  
Maren Wellenreuther ◽  
Jérémy Le Luyer ◽  
Denham Cook ◽  
Peter A. Ritchie ◽  
Louis Bernatchez
Keyword(s):  
Gene Expression ◽  
White Muscle ◽  
De Novo ◽  
Thermal Adaptation ◽  
Blood Parameters ◽  
Growth Responses ◽  
Rna Transcription ◽  
Immune Pathways ◽  
Model Fish Species ◽  
Model Fish

ABSTRACTIdentifying genes and pathways involved in domestication is critical to understand how species change in response to human-induced selection pressures. We experimentally manipulated temperature conditions for F1-hatchery and wild Australasian snapper (Chrysophrys auratus) for 18 days and measured differences in growth, white muscle RNA transcription and haematological blood parameters. Over 2.2 Gb paired-end reads were assembled de novo for a total set of 33,017 transcripts (N50 = 2,804). We found pronounced growth and gene expression differences between wild and domesticated individuals related to global developmental and immune pathways. Temperature modulated growth responses were linked to major pathways affecting metabolism, cell regulation and signalling. This study is the first step towards gaining an understanding of the changes occurring in the early stages of domestication, and the mechanisms underlying thermal adaptation and associated growth in poikilothermic vertebrates. Our study further provides the first transcriptome resources for studying biological questions in this non-model fish species.

Gene networks underlying functional sex in Sparidae (Pisces, Teleostei)

2018 ◽  
Author(s):  
Αλέξανδρος Τσακογιάννης
Keyword(s):  
Gene Expression ◽  
Sex Determination ◽  
Gene Networks ◽  
Expression Patterns ◽  
Gene Families ◽  
Male And Female ◽  
Dentex Dentex ◽  
The Common ◽  
Model Fish Species ◽  
Model Fish

The differences between sexes and the concept of sex determination have always fascinated, yet troubled philosophers and scientists. Among the animals that reproduce sexually, teleost fishes show a very wide repertoire of reproductive modes. Except for the gonochoristic species, fish are the only vertebrates in which hermaphroditism appears naturally. Hermaphroditism refers to the capability of an organism to reproduce both as male and female in its life cycle and there are various forms of it. In sequential hermaphroditism, an individual begins as female first and then can change sex to become male (protogyny), or vice versa (protandry). The diverse sex-phenotypes of fish are regulated by a variety of sex determination mechanisms, along a continuum of environmental and heritable factors. The vast majority of sexually dimorphic traits result from the differential expression of genes that are present in both sexes. To date, studies regarding the sex-specific differences in gene expression have been conducted mainly in sex determination systems of model fish species that are well characterized at the genomic level, with distinguishable heteromorphic sex chromosomes, exhibiting genetic sex determination and gonochorism. Among teleosts, the Sparidae family is considered to be one of the most diversified families regarding its reproductive systems, and thus is a unique model for comparative studies to understand the molecular mechanisms underlying different sexual motifs. In this study, using RNA sequencing, we studied the transcriptome from gonads and brains of both sexes in five sparid species, representatives of four different reproductive styles. Specifically, we explored the sex-specific expression patterns of a gonochoristic species: the common dentex Dentex dentex, two protogynous hermaphrodites: the red porgy Pagrus pagrus and the common pandora Pagellus erythrinus, the rudimentary hermaphrodite sharpsnout seabream Diplodus puntazzo, and the protandrous gilthead seabream Sparus aurata. We found minor sex-related expression differences indicating a more homogeneous and sexually plastic brain, whereas there was a plethora of sex biased gene expression in the gonads. The functional divergence of the two gonadal types is reflected in their transcriptomic profiles, in terms of the number of genes differentially expressed, as well as the expression magnitude (i.e. fold-change differences). The observation of almost double the number of up-regulated genes in males compared to females indicates a male-biased expression tendency. Focusing on the pathways and genes implicated in sex determination/differentiation, we aimed to unveil the molecular pathways through which these non-model fish species develop a masculine or a feminine character. We observed the implicated pathways and major gene families (e.g. Wnt/b-catenin pathway and Retinoic-acid signaling pathway, Notch, TGFβ) behind sex-biased expression and the recruitment of known sex-related genes either to male or female type of gonads in these fish. (e.g Dmrt1, Sox9, Sox3, Cyp19a, Filgla, Ctnnb1, Gsdf9, Stra6 etc.). We also carefully investigated the presence of genes reported to be involved in sex determination/differentiation mechanisms in other vertebrates and fish and compared their expression patterns in the species under study. The expression profiling exposed known candidate molecular-players/genes establishing the common female (Cyp19a1, Sox3, Figla, Gdf9, Cyp26a, Ctnnb1, Dnmt1, Stra6) and male identity (Dmrt1, Sox9, Dnmt3aa, Rarb, Raraa, Hdac8, Tdrd7) of the gonad in these sparids. Additionally, we focused on those contributing to a species-specific manner either to female (Wnt4a, Dmrt2a, Foxl2 etc.) or to male (Amh, Dmrt3a, Cyp11b etc.) characters, and discussed the expression patterns of factors that belong to important pathways and/or gene families in the SD context, in our species gonadal transcriptomes. Taken together, most of the studied genes form part of the cascade of sex determination, differentiation, and reproduction across teleosts. In this study, we focused on genes that are active when sex is established (sex-maintainers), revealing the basic “gene-toolkit” & gene-networks underlying functional sex in these five sparids. Comparing related species with alternative reproductive styles, we saw different combinations of genes with conserved sex-linked roles and some “handy” molecular players, in a “partially- conserved” or “modulated” network formulating the male and female phenotype. The knowledge obtained in this study and tools developed during the process have set the groundwork for future experiments that can improve the sex control of this species and help the in-deep understanding the complex process of sex differentiation in the more flexible multi-component systems as these studied here.

scholarly journals De Novo Transcriptome Analysis Reveals Potential Thermal Adaptation Mechanisms in the Cicada Hyalessa fuscata

Animals ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 2785
Author(s):  
Hoa Quynh Nguyen ◽  
Yuseob Kim ◽  
Yikweon Jang
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Heat Shock ◽  
Thermal Tolerance ◽  
De Novo ◽  
Expression Patterns ◽  
Thermal Adaptation ◽  
Urban Heat Islands ◽  
Cellular Damage ◽  
Acute Heat Stress

In metropolitan Seoul, populations of the cicada Hyalessa fuscata in hotter urban heat islands (“high UHIs”) exhibit higher thermal tolerance than those in cooler UHIs (“low UHIs”). We hypothesized that heat stress may activate the expression of genes that facilitate greater thermal tolerance in high-UHI cicadas than in those from cooler areas. Differences in the transcriptomes of adult female cicadas from high-UHI, low-UHI, and suburban areas were analyzed at the unheated level, after acute heat stress, and after heat torpor. No noticeable differences in unheated gene expression patterns were observed. After 10 min of acute heat stress, however, low-UHI and suburban cicadas expressed more heat shock protein genes than high-UHI counterparts. More specifically, remarkable changes in the gene expression of cicadas across areas were observed after heat torpor stimulus, as represented by a large number of up- and downregulated genes in the heat torpor groups compared with the 10 min acute heat stress and control groups. High-UHI cicadas expressed the most differentially expressed genes, followed by the low-UHI and suburban cicadas. There was a notable increase in the expression of heat shock, metabolism, and detoxification genes; meanwhile, immune-related, signal transduction, and protein turnover genes were downregulated in high-UHI cicadas versus the other cicada groups. These results suggested that under heat stress, cicadas inhabiting high-UHIs could rapidly express genes related to heat shock, energy metabolism, and detoxification to protect cells from stress-induced damage and to increase their thermal tolerance toward heat stress. The downregulation of apoptosis mechanisms in high-UHI cicadas suggested that there was less cellular damage, which likely contributed to their high tolerance of heat stress.

scholarly journals AAV-Mediated CRISPRi and RNAi Based Gene Silencing in Mouse Hippocampal Neurons

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 324
Author(s):  
Matthias Deutsch ◽  
Anne Günther ◽  
Rodrigo Lerchundi ◽  
Christine R. Rose ◽  
Sabine Balfanz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Initiation ◽  
Hippocampal Neurons ◽  
De Novo ◽  
Protein Biosynthesis ◽  
Physiological Role ◽  
High Specificity ◽  
Hcn Channels ◽  
Proliferating Cells ◽  
Neuronal Tissues

Uncovering the physiological role of individual proteins that are part of the intricate process of cellular signaling is often a complex and challenging task. A straightforward strategy of studying a protein’s function is by manipulating the expression rate of its gene. In recent years, the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/Cas9-based technology was established as a powerful gene-editing tool for generating sequence specific changes in proliferating cells. However, obtaining homogeneous populations of transgenic post-mitotic neurons by CRISPR/Cas9 turned out to be challenging. These constraints can be partially overcome by CRISPR interference (CRISPRi), which mediates the inhibition of gene expression by competing with the transcription machinery for promoter binding and, thus, transcription initiation. Notably, CRISPR/Cas is only one of several described approaches for the manipulation of gene expression. Here, we targeted neurons with recombinant Adeno-associated viruses to induce either CRISPRi or RNA interference (RNAi), a well-established method for impairing de novo protein biosynthesis by using cellular regulatory mechanisms that induce the degradation of pre-existing mRNA. We specifically targeted hyperpolarization-activated and cyclic nucleotide-gated (HCN) channels, which are widely expressed in neuronal tissues and play essential physiological roles in maintaining biophysical characteristics in neurons. Both of the strategies reduced the expression levels of three HCN isoforms (HCN1, 2, and 4) with high specificity. Furthermore, detailed analysis revealed that the knock-down of just a single HCN isoform (HCN4) in hippocampal neurons did not affect basic electrical parameters of transduced neurons, whereas substantial changes emerged in HCN-current specific properties.

scholarly journals Malpigmentation of Common Sole (Solea solea) during Metamorphosis Is Associated with Differential Synaptic-Related Gene Expression

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2273
Author(s):  
Menelaos Kavouras ◽  
Emmanouil E. Malandrakis ◽  
Ewout Blom ◽  
Kyriaki Tsilika ◽  
Theodoros Danis ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nervous System ◽  
De Novo ◽  
Close Association ◽  
Ionic Channels ◽  
Long Term Potentiation ◽  
General Term ◽  
The Difference ◽  
Common Sole

In farmed flatfish, such as common sole, color disturbances are common. Dyschromia is a general term that includes the color defects on the blind and ocular sides of the fish. The purpose was to examine the difference in gene expression between normal pigmented and juveniles who present ambicoloration. The analysis was carried out with next-generation sequencing techniques and de novo assembly of the transcriptome. Transcripts that showed significant differences (FDR < 0.05) in the expression between the two groups, were related to those of zebrafish (Danio rerio), functionally identified, and classified into categories of the gene ontology. The results revealed that ambicolorated juveniles exhibit a divergent function, mainly of the central nervous system at the synaptic level, as well as the ionic channels. The close association of chromophore cells with the growth of nerve cells and the nervous system was recorded. The pathway, glutamate binding–activation of AMPA and NMDA receptors–long-term stimulation of postsynaptic potential–LTP (long term potentiation)–plasticity of synapses, appears to be affected. In addition, the development of synapses also seems to be affected by the interaction of the LGI (leucine-rich glioma inactivated) protein family with the ADAM (a disintegrin and metalloprotease) ones.

scholarly journals The brain transcriptome of the wolf spider, Schizocosa ocreata

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Daniel Stribling ◽  
Peter L. Chang ◽  
Justin E. Dalton ◽  
Christopher A. Conow ◽  
Malcolm Rosenthal ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Model Organisms ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Wolf Spiders ◽  
Schizocosa Ocreata ◽  
Genomic Studies ◽  
The Brain

Abstract Objectives Arachnids have fascinating and unique biology, particularly for questions on sex differences and behavior, creating the potential for development of powerful emerging models in this group. Recent advances in genomic techniques have paved the way for a significant increase in the breadth of genomic studies in non-model organisms. One growing area of research is comparative transcriptomics. When phylogenetic relationships to model organisms are known, comparative genomic studies provide context for analysis of homologous genes and pathways. The goal of this study was to lay the groundwork for comparative transcriptomics of sex differences in the brain of wolf spiders, a non-model organism of the pyhlum Euarthropoda, by generating transcriptomes and analyzing gene expression. Data description To examine sex-differential gene expression, short read transcript sequencing and de novo transcriptome assembly were performed. Messenger RNA was isolated from brain tissue of male and female subadult and mature wolf spiders (Schizocosa ocreata). The raw data consist of sequences for the two different life stages in each sex. Computational analyses on these data include de novo transcriptome assembly and differential expression analyses. Sample-specific and combined transcriptomes, gene annotations, and differential expression results are described in this data note and are available from publicly-available databases.

scholarly journals Viral Gene Expression Patterns in Human Herpesvirus 6B-Infected T Cells

2002 ◽  
Vol 76 (15) ◽  
pp. 7578-7586 ◽  
Author(s):  
Bodil Øster ◽  
Per Höllsberg
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Protein Synthesis ◽  
De Novo ◽  
Expression Patterns ◽  
Human Herpesvirus ◽  
Viral Gene Expression ◽  
Polymerase Activity ◽  
Viral Gene ◽  
De Novo Protein Synthesis

ABSTRACT Herpesvirus gene expression is divided into immediate-early (IE) or α genes, early (E) or β genes, and late (L) or γ genes on the basis of temporal expression and dependency on other gene products. By using real-time PCR, we have investigated the expression of 35 human herpesvirus 6B (HHV-6B) genes in T cells infected by strain PL-1. Kinetic analysis and dependency on de novo protein synthesis and viral DNA polymerase activity suggest that the HHV-6B genes segregate into six separate kinetic groups. The genes expressed early (groups I and II) and late (groups V and VI) corresponded well with IE and L genes, whereas the intermediate groups III and IV contained E and L genes. Although HHV-6B has characteristics similar to those of other roseoloviruses in its overall gene regulation, we detected three B-variant-specific IE genes. Moreover, genes that were independent of de novo protein synthesis clustered in an area of the viral genome that has the lowest identity to the HHV-6A variant. The organization of IE genes in an area of the genome that differs from that of HHV-6A underscores the distinct differences between HHV-6B and HHV-6A and may provide a basis for further molecular and immunological analyses to elucidate their different biological behaviors.

scholarly journals Troglitazone, an Insulin-Sensitizing Thiazolidinedione, Represses Combined Stimulation by LH and Insulin of de Novo Androgen Biosynthesis by Thecal Cells in Vitro

2002 ◽  
Vol 87 (3) ◽  
pp. 1129-1133 ◽  
Author(s):  
Johannes D. Veldhuis ◽  
George Zhang ◽  
James C. Garmey
Keyword(s):  
Gene Expression ◽  
Polycystic Ovarian Syndrome ◽  
De Novo ◽  
Drug Concentrations ◽  
Thecal Cells ◽  
Cyp17 Gene ◽  
Pparγ Agonist ◽  
Ovarian Syndrome ◽  
Prostaglandin J2

Polycystic ovarian syndrome (anovulatory hyperandrogenism) is marked by adolescent onset of systemic hyperinsulinism, oligoovulation, hirsutism, excessive LH and androgen secretion, and variable reduction in fertility. Insulin and LH are believed to act in concert to promote ovarian androgen hypersecretion in this disorder. Administration of troglitazone, an insulin-sensitizing agent and putative PPARγ agonist, can decrease hyperinsulinism, suppress T production, and ameliorate oligoovulation in some women with this endocrinopathy. The present study tests the hypothesis that troglitazone directly inhibits de novo androgen biosynthesis stimulated jointly by LH and insulin in primary cultures of (porcine) thecal cells. We show that troglitazone dose-dependently antagonizes LH/insulin’s combined stimulation of androstenedione and T production by thecal cells in vitro. Consistent steroidogenic inhibition of 80–95% was achieved at drug concentrations of 3–6.8 μm (P &lt; 0.001). Exposure of thecal cells to the thiazolidinedione derivative also blocked bihormonally stimulated accumulation of CYP17 (cytochrome P450 17 α-hydroxylase/C17–20 lyase) gene expression, as reflected by decreased accumulation of cognate heterogeneous nuclear RNA and mRNA (by 30–65%; P &lt; 0.05). Moreover, troglitazone suppressed LH/insulin-induced phosphorylation of the 52-kDa immunoprecipitated CYP17 enzyme by 88% (P &lt; 0.001). A putative natural agonist of PPARγ nuclear transcription, 15-deoxy-δ-12,14-prostaglandin J2, also inhibited LH/insulin-driven androstenedione biosynthesis and CYP17 gene expression in thecal cells. In conclusion, a synthetic thiazolidinedione (troglitazone) and a natural ligand of PPARγ (15-deoxy-δ-12,14-prostaglandin J2) effectively impede the concerted stimulation by LH and insulin of in vitro thecal cell androgen production, CYP17 gene expression, and CYP17 protein phosphorylation. This ensemble of inhibitory actions on LH/insulin-stimulated steroidogenesis offers a plausible mechanistic basis for at least part of the observed clinical efficacy of troglitazone in mitigating androgen excess in women with polycystic ovarian syndrome.

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