scholarly journals Mid and hindgut transcriptome profiling analysis of Atlantic salmon ( Salmon salar ) under unpredictable chronic stress

2020 ◽  
Vol 7 (2) ◽  
pp. 191480
Author(s):  
Signe Dille Løvmo ◽  
Angelico Madaro ◽  
Paul Whatmore ◽  
Tora Bardal ◽  
Mari-Ann Ostensen ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Chronic Stress ◽  
Transcriptome Profiling ◽  
Intestinal Morphology ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Negative Consequences ◽  
Membrane Structures ◽  
Apoptotic Pathway ◽  
Salmon Parr

The intestinal epithelium is a selectively permeable barrier for nutrients, electrolytes and water, while maintaining effective protection against pathogens. Combinations of stressors throughout an animal's life, especially in agriculture and aquaculture settings, may affect the regular operativity of this organ with negative consequences for animal welfare. In the current study, we report the effects of a three-week unpredictable chronic stress (UCS) period on the intestinal morphology and transcriptome response of Atlantic salmon ( Salmon salar ) parr midgut and hindgut. Midgut and hindgut from both control and UCS fish were collected for histology and RNA-sequencing analysis to identify respective changes in the membrane structures and putative genes and pathways responding to UCS. Histological analysis did not show any significant effect on morphometric parameters. In the midgut, 1030 genes were differentially expressed following UCS, resulting in 279 genes which were involved in 13 metabolic pathways, including tissue repair pathways. In the hindgut, following UCS, 591 differentially expressed genes were detected with 426 downregulated and 165 upregulated. A total of 53 genes were related to three pathways. Downregulated genes include cellular senescence pathways, p53 signalling and cytokine–cytokine receptor pathways. The overall results corroborate that salmon parr were at least partly habituating to the UCS treatment. In midgut, the main upregulation was related to cell growth and repair, while in the hindgut there were indications of the activated apoptotic pathway, reduced cell repair and inhibited immune/anti-inflammatory capacity. This may be the trade-off between habituating to UCS and health resilience. This study suggests possible integrated genetic regulatory mechanisms that are tuned when farmed Atlantic salmon parr attempt to cope with UCS.

scholarly journals Transcriptome Profiling Reveals Inhibitory Effect of Down-regulated ZBTB38 gene on the Transcriptional Regulation of Tumor Cells Proliferation

2018 ◽  
Author(s):  
Jie Chen ◽  
Chaofeng Xing ◽  
Haosen Wang ◽  
Zengmeng Zhang ◽  
Daolun Yu ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Tumor Cells ◽  
Differentially Expressed Genes ◽  
Zinc Finger Protein ◽  
Enrichment Analysis ◽  
Transcriptome Profiling ◽  
Inhibitory Effect ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Sequencing Analysis

AbstractTranscription factor ZBTB38 belongs to the zinc finger protein family and contains the typical BTB domains. Only several predicted BTB domain-containing proteins encoded in the human genome have been functionally characterized. No relevant studies have been reported concerning the effect of down-regulated ZBTB38 gene expression on tumor cells through transcriptome analysis. In the present study, 2,438 differentially expressed genes in ZBTB38−/− SH-SY5Y cells were obtained via high-throughput transcriptome sequencing analysis, 83.5% of which was down-regulated. Furthermore, GO functional clustering and KEGG pathway enrichment analysis of these differentially expressed genes (DEGs) revealed that the knocked-down transcription factor ZBTB38 interacted with p53 and arrested cell cycles to inhibit the proliferation of the tumor cells. Besides, it also significantly down-regulated the expressions of PTEN, a “molecular switch” of the PI3K/Akt signaling pathway, and RB1CC1, the key gene for autophagy initiation, and blocked autophagy to accelerate the apoptosis of tumor cells. ZBTB38−/− SH-SY5Y cells were investigated at the whole transcriptome level and key DEGs were screened in the present study for the first time, providing a theoretical foundation for exploring the molecular mechanism of inhibition of tumor cell proliferation and targeted anti-tumor therapies.

scholarly journals Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hangxia Jin ◽  
Xiaomin Yu ◽  
Qinghua Yang ◽  
Xujun Fu ◽  
Fengjie Yuan
Keyword(s):  
Developmental Stage ◽  
Phytic Acid ◽  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Defense Mechanisms ◽  
Developmental Stages ◽  
Sucrose Metabolism ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Seed Developmental Stage

AbstractPhytic acid (PA) is a major antinutrient that cannot be digested by monogastric animals, but it can decrease the bioavailability of micronutrients (e.g., Zn and Fe). Lowering the PA content of crop seeds will lead to enhanced nutritional traits. Low-PA mutant crop lines carrying more than one mutated gene (lpa) have lower PA contents than mutants with a single lpa mutant gene. However, little is known about the link between PA pathway intermediates and downstream regulatory activities following the mutation of these genes in soybean. Consequently, we performed a comparative transcriptome analysis using an advanced generation recombinant inbred line with low PA levels [2mlpa (mips1/ipk1)] and a sibling line with homozygous non-mutant alleles and normal PA contents [2MWT (MIPS1/IPK1)]. An RNA sequencing analysis of five seed developmental stages revealed 7945 differentially expressed genes (DEGs) between the 2mlpa and 2MWT seeds. Moreover, 3316 DEGs were associated with 128 metabolic and signal transduction pathways and 4980 DEGs were annotated with 345 Gene Ontology terms related to biological processes. Genes associated with PA metabolism, photosynthesis, starch and sucrose metabolism, and defense mechanisms were among the DEGs in 2mlpa. Of these genes, 36 contributed to PA metabolism, including 22 genes possibly mediating the low-PA phenotype of 2mlpa. The expression of most of the genes associated with photosynthesis (81 of 117) was down-regulated in 2mlpa at the late seed developmental stage. In contrast, the expression of three genes involved in sucrose metabolism was up-regulated at the late seed developmental stage, which might explain the high sucrose content of 2mlpa soybeans. Furthermore, 604 genes related to defense mechanisms were differentially expressed between 2mlpa and 2MWT. In this study, we detected a low PA content as well as changes to multiple metabolites in the 2mlpa mutant. These results may help elucidate the regulation of metabolic events in 2mlpa. Many genes involved in PA metabolism may contribute to the substantial decrease in the PA content and the moderate accumulation of InsP3–InsP5 in the 2mlpa mutant. The other regulated genes related to photosynthesis, starch and sucrose metabolism, and defense mechanisms may provide additional insights into the nutritional and agronomic performance of 2mlpa seeds.

scholarly journals Next-Generation Sequencing Analysis of the Tineola bisselliella Larval Gut Transcriptome Reveals Candidate Enzymes for Keratin Digestion

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1113
Author(s):  
Michael Schwabe ◽  
Sven Griep ◽  
Henrike Schmidtberg ◽  
Rudy Plarre ◽  
Alexander Goesmann ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Disulfide Bonds ◽  
Differentially Expressed ◽  
Intestinal Microbiome ◽  
Sequencing Analysis ◽  
High Quality ◽  
Transcriptomic Data ◽  
Next Generation Sequencing Analysis ◽  
Generation Sequencing ◽  
Tineola Bisselliella

The clothes moth Tineola bisselliella is one of a few insects that can digest keratin, leading to the destruction of clothing, textiles and artwork. The mechanism of keratin digestion is not yet fully understood, partly reflecting the lack of publicly available genomic and transcriptomic data. Here we present a high-quality gut transcriptome of T. bisselliella generated from larvae reared on keratin-rich and keratin-free diets. The overall transcriptome consists of 428,221 contigs that were functionally annotated and screened for candidate enzymes involved in keratin utilization. As a mechanism for keratin digestion, we identified cysteine synthases, cystathionine β-synthases and cystathionine γ-lyases. These enzymes release hydrogen sulfite, which may reduce the disulfide bonds in keratin. The dataset also included 27 differentially expressed contigs with trypsin domains, among which 20 were associated with keratin feeding. Finally, we identified seven collagenases that were upregulated on the keratin-rich diet. In addition to this enzymatic repertoire potentially involved in breaking down keratin, our analysis of poly(A)-enriched and poly(A)-depleted transcripts suggested that T. bisselliella larvae possess an unstable intestinal microbiome that may nevertheless contribute to keratin digestion.

Transcriptome Profiling of Long Non-coding RNAs During the Atlantic Salmon Smoltification Process

2021 ◽  
Vol 23 (2) ◽  
pp. 308-320
Author(s):  
Valentina Valenzuela-Muñoz ◽  
Juan Antonio Váldes ◽  
Cristian Gallardo-Escárate
Keyword(s):  
Atlantic Salmon ◽  
Transcriptome Profiling ◽  
Non Coding Rnas

Interhabitat and instream movements of large Atlantic salmon parr in a Newfoundland watershed in winter

2003 ◽  
Vol 63 (5) ◽  
pp. 1208-1218 ◽  
Author(s):  
M. J. Robertson ◽  
K. D. Clarke ◽  
D. A. Scruton ◽  
J. A. Brown
Keyword(s):  
Atlantic Salmon ◽  
Salmon Parr ◽  
Atlantic Salmon Parr

Feeding by Hatchery-Reared and Wild Atlantic Salmon (Salmo salar) Parr in Streams

1979 ◽  
Vol 36 (11) ◽  
pp. 1408-1412 ◽  
Author(s):  
A. J. Sosiak ◽  
R. G. Randall ◽  
J. A. McKenzie
Keyword(s):  
Atlantic Salmon ◽  
Key Words ◽  
Salmo Salar ◽  
Food Selection ◽  
Stomach Contents ◽  
Stomach Fullness ◽  
Size Dependent ◽  
Atlantic Salmon Salmo Salar ◽  
Feeding Experience ◽  
Salmon Parr

Hatchery-reared Atlantic salmon (Salmo salar) parr were captured 1–3 mo after release in streams, along with wild parr from the same streams. Identification of their stomach contents showed total number of organisms and number of taxa per stomach were greater and there was a higher index of stomach fullness in wild than in hatchery parr resident ≤ 2 mo in a stream. Wild parr consumed more Brachycentridae, Hydroptilidae, Diptera, and Plecoptera than did hatchery parr, but sometimes less Odontoceridae and Heptageniidae. These differences may have arisen from size-dependent food selection, the effects of feeding experience, or possible microhabitat differences between wild and hatchery parr. Key words: salmon parr, hatchery-reared, wild, feeding

Degradation of DDT in Atlantic Salmon (Salmo salar)

1968 ◽  
Vol 25 (11) ◽  
pp. 2321-2326 ◽  
Author(s):  
G. L. Greer ◽  
U. Paim
Keyword(s):  
Atlantic Salmon ◽  
Thin Layer ◽  
Thin Layer Chromatography ◽  
Salmo Salar ◽  
Aqueous Suspensions ◽  
Atlantic Salmon Salmo Salar ◽  
Salmon Parr ◽  
Layer Chromatography ◽  
Atlantic Salmon Parr

As indicated by thin-layer chromatography, hatchery-reared Atlantic salmon parr degraded DDT, absorbed from aqueous suspensions, to DDE and TDE within 9 hr. DDT adsorbed on external surfaces of the salmon was not degraded.

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