Transcriptomic Analysis of Metabolic Pathways in Milkfish That Respond to Salinity and Temperature Changes

Hu, Yau Chung; Kang, Can; Tang, Cheng; Lee, Tsung‐Han

doi:10.1371/journal.pone.0134959

Cited by 44 publications

(33 citation statements)

References 57 publications

(66 reference statements)

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“…(1) bias towards upregulation of gene expression, (2) cellular stress responses including upregulation of genes involved in protein folding, protein ubiquitination, proteasome and DNA repair functions, (3) upregulation of genes involved in mRNA expression, RNA processing and pre-mRNA splicing, and (4) enriched differential expression of genes involved in metabolic pathways (Itoi et al, 2003;Gracey et al, 2004;Vornanen et al, 2005;Chou et al, 2008;Castilho et al, 2009;Vergauwen et al, 2010;Long et al, 2012Long et al, , 2013Scott and Johnston, 2012;Jayasundara et al, 2013Jayasundara et al, , 2015Rebl et al, 2013;Bilyk and Cheng, 2014;Mininni et al, 2014;Morris et al, 2014;Wang et al, 2014;Hu et al, 2015;Liang et al, 2015;Verleih et al, 2015;Healy et al, 2017;Ikeda et al, 2017;Metzger and Schulte, 2018). However, the direction of differential expression of metabolic genes is species-specific and likely indicates differences in metabolic strategy (i.e.…”

Section: Role Of Changes In Mrna Splicing Patterns In Plasticity As Amentioning

confidence: 99%

Patterns of alternative splicing in response to cold acclimation in fish

Healy

Schulte

2019

Journal of Experimental Biology

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Phenotypic plasticity is an important aspect of an organism's response to environmental change that often requires the modulation of gene expression. These changes in gene expression can be quantitative, as a result of increases or decreases in the amounts of specific transcripts, or qualitative, as a result of the expression of alternative transcripts from the same gene (e.g. via alternative splicing of pre-mRNAs). Although the role of quantitative changes in gene expression in phenotypic plasticity is well known, relatively few studies have examined the role of qualitative changes. Here, we use skeletal muscle RNA-seq data from Atlantic killifish (Fundulus heteroclitus), threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio) to investigate the extent of qualitative changes in gene expression in response to cold acclimation. Fewer genes demonstrated alternative splicing than differential expression as a result of cold acclimation; however, differences in splicing were detected for 426 to 866 genes depending on species, indicating that large numbers of qualitative changes in gene expression are associated with cold acclimation. Many of these alternatively spliced genes were also differentially expressed, and there was functional enrichment for involvement in muscle contraction among the genes demonstrating qualitative changes in response to cold acclimation. Additionally, there was a common group of 29 genes with cold-acclimation-mediated changes in splicing in all three species, suggesting that there may be a set of genes with expression patterns that respond qualitatively to prolonged exposure to cold temperatures across fishes.

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Section: Role Of Changes In Mrna Splicing Patterns In Plasticity As Amentioning

confidence: 99%

Patterns of alternative splicing in response to cold acclimation in fish

Healy

Schulte

2019

Journal of Experimental Biology

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“…Bacteriocins are ribosomally synthesized cationic antimicrobial peptides (CAMPs) produced by bacteria that inhibit the growth of a broad spectrum of pathogens (Heng et al, 2007). Some bacteria that produce bacteriocins are considered food grade by the United States Food and Drug Administration (FDA) (Chen and Hoover, 2006), making them useful for food preservation (Hu et al, 2015). Although, there are a number of bacteriocins that have been studied for their antimicrobial properties, nisin and pediocin are the only commercially available, FDA-approved bacteriocins used in a variety of food products (Chen and Hoover, 2006;Garsa et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Nevertheless, She Resisted – Role of the Environment on Listeria monocytogenes Sensitivity to Nisin Treatment in a Laboratory Cheese Model

et al. 2020

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The growth of Listeria monocytogenes on refrigerated, ready-to-eat food products is a major health and economic concern. The natural antimicrobial nisin targets the bacterial cell wall and can be used to inhibit L. monocytogenes growth on cheese. Cell wall composition and structure, and therefore the efficacy of cell wall acting control strategies, can be severely affected by environmental and stress conditions. The goal of this study was to determine the effect of a range of pH and temperatures on the efficacy of nisin against several strains of L. monocytogenes in a lab-scale, cheese model. Cheese was made with or without the addition of nisin at different pH and then inoculated with L. monocytogenes; L. monocytogenes numbers were quantified after 1, 7, and 14 days of incubation at 6, 14, or 22 • C. While our data show that nisin treatment is able to reduce L. monocytogenes numbers, at least initially, growth of this pathogen can occur even in the presence of nisin, especially when cheese is stored at higher temperatures. Several environmental factors were found to affect nisin efficacy against L. monocytogenes. For example, nisin is more effective when cheese is stored at lower temperatures. Nisin is also more effective when cheese is made at higher pH (6 and 6.5), compared to cheese made at pH 5.5, and this effect is at least partially due to the activity of cell envelope modification genes dltA and mprF. Serotype was also found to affect nisin efficacy against L. monocytogenes; serotype 4b strains showed lower susceptibility to nisin treatment compared to serotype 1/2 strains. Overall, our results highlight the importance of considering environmental conditions specific to a food matrix when developing and applying nisin-based intervention strategies against L. monocytogenes.

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“…Partial DNA sequence presenting homology to Ccprdx6 was identified from the milkfish NGS database (Hu et al, 2015). The partial fragment of the Ccprdx6 gene was amplified by PCR using cDNA as a template, and the primers were designed by Primer 3 Plus (http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi) based on the highly conserved region compared with that of other teleosts (Supplementary Table 1).…”

Section: Methodsmentioning

confidence: 99%

“…The proteomic analyses of milkfish livers under hypothermal stress detected a pI shift of two Prdx6 protein spots (Chang et al, 2016). From the transcriptome database of milkfish with low-temperature treatments (Hu et al, 2015), the partial sequence of Ccprdx6 could be identified.…”

Section: Introductionmentioning

confidence: 99%

The Antioxidant Peroxiredoxin 6 (Prdx6) Exhibits Different Profiles in the Livers of Seawater- and Fresh Water-Acclimated Milkfish, Chanos chanos, upon Hypothermal Challenge

Chang

Lee

2016

Front. Physiol.

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A tropical species, the euryhaline milkfish (Chanos chanos), is a crucial economic species in Southeast Asia and is intolerant of water temperature below 12°C. Large numbers of milkfish die during cold periods in winter. Hypothermal environments usually increase oxidative stress in teleosts, and the liver is the major organ for anti-oxidative responses in the body. Peroxiredoxin-6 (Prdx6) in mammals is a multi-functional enzyme and acts as both glutathione peroxidase, phospholipase A2 and acyl-transferase for maintenance of redox status and prevention of cell membrane peroxidation. Prdx6 can protect cells from oxidant-induced membrane damage by translocating the Prdx6 protein from the cytosol to the membrane. Upon cold stress, Ccprdx6 transcript levels were up-regulated after 24 h and 96 h in livers of fresh water (FW)- and seawater (SW)-acclimated milkfish, respectively. In the hypothermal FW group, the Prdx6 protein was up-regulated in the cytosol of hepatocytes with a similar role as glutathione peroxidase to reduce oxidative stress upon hypothermal challenge. Conversely, in hypothermal SW milkfish, total Prdx6 protein was down-regulated. However, cytosolic Prdx6 protein was translocated to the membrane, using the ability of phospholipase A2 to stabilize the membrane redox state. Moreover, H2O2 content was increased in FW-acclimated milkfish livers upon hypothermal challenge. Ex vivo H2O2 treatment of milkfish livers also induced Ccprdx6 transcriptional expression, which provided more evidence of the antioxidant role of milkfish Prdx6. Taken together, upon hypothermal challenge, greater oxidative stress in livers of FW-acclimated milkfish rather than SW-acclimated individuals led to different profiles of hepatic CcPrdx6 expression between the FW and SW group. The results indicated that CcPrdx6 played the role of antioxidant with different mechanisms, i.e., binding to reactive oxygen species and stabilizing membrane fluidity, in livers of hypothermal FW and SW milkfish, respectively.

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Transcriptomic Analysis of Metabolic Pathways in Milkfish That Respond to Salinity and Temperature Changes

Cited by 44 publications

References 57 publications

Patterns of alternative splicing in response to cold acclimation in fish

Patterns of alternative splicing in response to cold acclimation in fish

Nevertheless, She Resisted – Role of the Environment on Listeria monocytogenes Sensitivity to Nisin Treatment in a Laboratory Cheese Model

The Antioxidant Peroxiredoxin 6 (Prdx6) Exhibits Different Profiles in the Livers of Seawater- and Fresh Water-Acclimated Milkfish, Chanos chanos, upon Hypothermal Challenge

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