Transcriptome data of Epinephelus fuscoguttatus infected by Vibrio vulnificus

Jazamuddin, Fahmeeda Mohamad; Aizat, Wan Mohd; Goh, Hoe-Han; Low, Chen Fei; Baharum, Syarul Nataqain

doi:10.1016/j.dib.2017.11.024

Cited by 6 publications

(6 citation statements)

References 3 publications

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“…Then, the transcriptome database was used for data interpretation and protein identification. The title of reference was transcriptome data of Epinephelus fuscoguttatus infected by Vibrio vulnificus (Jazamuddin et al 2018). The protein database was sourced from http://www.ncbi.nlm.nih.gov/sra/ SRX3067303.…”

Section: Protein Database Searching and Analysismentioning

confidence: 99%

Proteomics study on the protective mechanism of soybean isoflavone against inflammation injury of bovine mammary epithelial cells induced by Streptococcus agalactiae

Niu

Zhang

et al. 2021

Cell Stress and Chaperones

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This study aimed to verify the anti-inflammatory effect of soybean isoflavones (SI) on the inflammatory response induced by Streptococcus agalactiae (S. agalactiae) of bovine mammary epithelial cells (bMECs) and to elucidate its possible mechanism. BMECs were pretreated with SI of different concentrations (20, 40, 60, 80, 100 μg/mL) for 0.5, 3, 6, 9, 12, 15, 18, 24 h. And then, S. agalactiae was used to infect bMECs for 6 h (MOI = 50:1) to establish the inflammation model. Cell viability, growth curves of S. agalactiae, cytotoxicity, and S. agalactiae invasion rate were determined. A proteomics technique was used to further detect differential proteins and enrichment pathways. SI (40 μg/mL) improved the viability of bMECs at 12 h (p < 0.05) and 60 and 80 μg/mL of SI greater (p < 0.01). Moreover, 60 μg/mL of SI protects cells from bacterial damage (p < 0.05). SI could inhibit S. agalactiae growth and internalization into bMECs in a time-and dose-dependent manner. In addition, proteomics results showed that 133 proteins were up-regulated and 89 proteins were down-regulated significantly. The differentially significantly expressed proteins (DSEPs) were mainly related to cell proliferation, differentiation, apoptosis, and migration. GO annotation showed that 222 DSEPs were divided into 23 biological processes (BP) terms, 14 cell components (CC) terms, and 12 molecular functions (MF) terms. DSEPs were significantly enriched in 10 pathways, of which the immune pathway was the main enrichment pathway.

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Section: Protein Database Searching and Analysismentioning

confidence: 99%

Proteomics study on the protective mechanism of soybean isoflavone against inflammation injury of bovine mammary epithelial cells induced by Streptococcus agalactiae

Niu

Zhang

et al. 2021

Cell Stress and Chaperones

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“…With the advancement and improvement of sequencing technologies, genome and transcriptome sequencing has become the approached method in understanding microbial interactions with the environment [ 58 , 59 ], animal hosts [ 60 ] and plant hosts [ 61 , 62 ]. Currently, the genomes of five pathogenic strains of G. boninense have been sequenced: two strains isolated from Indonesia, i.e., the strains NJ3 and G3 [ 63 , 64 ]; and three strains isolated from Malaysia, i.e., PER71, BRIUMSc [ 65 ] and FGV-M [ 66 ].…”

Section: G Boninense Multi-omics Datamentioning

confidence: 99%

Review Update on the Life Cycle, Plant–Microbe Interaction, Genomics, Detection and Control Strategies of the Oil Palm Pathogen Ganoderma boninense

Bharudin

Wahab

Samad

et al. 2022

Biology

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Plant pathogens are key threats to agriculture and global food security, causing various crop diseases that lead to massive economic losses. Palm oil is a commodity export of economic importance in Southeast Asia, especially in Malaysia and Indonesia. However, the sustainability of oil palm plantations and production is threatened by basal stem rot (BSR), a devastating disease predominantly caused by the fungus Ganoderma boninense Pat. In Malaysia, infected trees have been reported in nearly 60% of plantation areas, and economic losses are estimated to reach up to ~USD500 million a year. This review covers the current knowledge of the mechanisms utilized by G. boninense during infection and the methods used in the disease management to reduce BSR, including cultural practices, chemical treatments and antagonistic microorganism manipulations. Newer developments arising from multi-omics technologies such as whole-genome sequencing (WGS) and RNA sequencing (RNA-Seq) are also reviewed. Future directions are proposed to increase the understanding of G. boninense invasion mechanisms against oil palm. It is hoped that this review can contribute towards an improved disease management and a sustainable oil palm production in this region.

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“…Meanwhile, in our previous study, Illumina HiSeq TM 4000 was used to obtain the raw transcriptome data before it was trimmed to a total of 437,186,232 clean read sequences. With this transcriptome data, the immune-related genes that play roles in the immune response mechanisms of Epinephelus fuscoguttatus against Vibrio vulnificus infection can be determined (Jazamuddin et al, 2018). As in Epinephelus coioides, gene Bcl-2-associated anthanogene 5 (BAG5) which known as a molecular chaperone can bind to the Bcl-2 and modulate the cell survival of the fish.…”

Section: Transcriptomicsmentioning

confidence: 99%

Integration of Omics Tools for Understanding the Fish Immune Response Due to Microbial Challenge

et al. 2021

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Nowadays, fish production through aquaculture and wild capture is escalating due to the higher fish protein demand for human consumption. Thus, the needs for fish products to be improved in scale and quality are becoming increasingly important to meet the nutrition requirements. The negative impacts caused by pathogens infection both in hatchery and grow-out ponds, have resulted in low aquaculture productivity and economic losses for the farmers. Therefore, a systematic study exploring relevant omics datasets through a systems biology approach will enable scientist to describe the complexity and characteristics of interactions in the host-pathogen network, leading to identifying new targets or biomarkers for diseases infection caused by bacteria, viruses, and parasites. The use of different approaches and emerging technologies as a powerful tool in obtaining a new knowledge for sustainable aquaculture production has been increasingly applied by many researchers over the years. In this paper, several omics approaches used to assess the fish immune response were reviewed. A brief description is provided for the omics approaches applicable to aquacultures, such as genomics, transcriptomics, proteomics, and metabolomics. Each tool used are contributes to develop better treatment and prevention strategies to overcome aquaculture disease due to the microbial infections. In genomics and transcriptomics analysis, their parallel approach involving gene expression studies play important role in identifying immune-related genes of the host, response to infectious diseases. While for proteomics and metabolomics approaches, these omics will provide information on the biomarker discovery and understanding the immune-related biosynthetic pathway during pathogen infection. Additionally, examples of the integrative analysis of multi-omics tools required for researchers to better understand the biological systems of aquatic animals especially fish, will also be provided.

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Transcriptome data of Epinephelus fuscoguttatus infected by Vibrio vulnificus

Cited by 6 publications

References 3 publications

Proteomics study on the protective mechanism of soybean isoflavone against inflammation injury of bovine mammary epithelial cells induced by Streptococcus agalactiae

Proteomics study on the protective mechanism of soybean isoflavone against inflammation injury of bovine mammary epithelial cells induced by Streptococcus agalactiae

Review Update on the Life Cycle, Plant–Microbe Interaction, Genomics, Detection and Control Strategies of the Oil Palm Pathogen Ganoderma boninense

Integration of Omics Tools for Understanding the Fish Immune Response Due to Microbial Challenge

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