scholarly journals Transcriptome Analysis Elucidates the Key Responses of Bryozoan Fredericella sultana during the Development of Tetracapsuloides bryosalmonae (Myxozoa)

2020 ◽  
Vol 21 (16) ◽  
pp. 5910
Author(s):  
Gokhlesh Kumar ◽  
Reinhard Ertl ◽  
Jerri L. Bartholomew ◽  
Mansour El-Matbouli
Keyword(s):  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Ribosome Biogenesis ◽  
Protein Localization ◽  
Transcriptional Profiling ◽  
Innate Immune ◽  
Initiation Factor ◽  
Primary Host ◽  
Tetracapsuloides Bryosalmonae ◽  
Fredericella Sultana

Bryozoans are sessile, filter-feeding, and colony-building invertebrate organisms. Fredericella sultana is a well known primary host of the myxozoan parasite Tetracapsuloides bryosalmonae. There have been no attempts to identify the cellular responses induced in F. sultana during the T. bryosalmonae development. We therefore performed transcriptome analysis with the aim of identifying candidate genes and biological pathways of F. sultana involved in the response to T. bryosalmonae. A total of 1166 differentially up- and downregulated genes were identified in the infected F. sultana. Gene ontology of biological processes of upregulated genes pointed to the involvement of the innate immune response, establishment of protein localization, and ribosome biogenesis, while the downregulated genes were involved in mitotic spindle assembly, viral entry into the host cell, and response to nitric oxide. Eukaryotic Initiation Factor 2 signaling was identified as a top canonical pathway and MYCN as a top upstream regulator in the differentially expressed genes. Our study provides the first transcriptional profiling data on the F. sultana zooid’s response to T. bryosalmonae. Pathways and upstream regulators help us to understand the complex interplay in the infected F. sultana. The results will facilitate the elucidation of innate immune mechanisms of bryozoan and will lay a foundation for further analyses on bryozoan-responsive candidate genes, which will be an important resource for the comparative analysis of gene expression in bryozoans.

scholarly journals First transcriptome analysis of bryozoan Fredericella sultana, the primary host of myxozoan parasite Tetracapsuloides bryosalmonae

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9027 ◽  
Author(s):  
Gokhlesh Kumar ◽  
Reinhard Ertl ◽  
Jerri L. Bartholomew ◽  
Mansour El-Matbouli
Keyword(s):  
Functional Genomics ◽  
Molecular Mechanisms ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Gc Content ◽  
Cdna Libraries ◽  
Primary Host ◽  
Myxozoan Parasite ◽  
Tetracapsuloides Bryosalmonae ◽  
Fredericella Sultana

Bryozoans are aquatic invertebrate moss animals that are found worldwide. Fredericella sultana is a freshwater bryozoan and is the most common primary host of myxozoan parasite, Tetracapsuloides bryosalmonae. However, limited genomic resources are available for this bryozoan, which hampers investigations into the molecular mechanisms of host-parasite interactions. To better understand these interactions, there is a need to build a transcriptome dataset of F. sultana, for functional genomics analysis by large-scale RNA sequencing. Total RNA was extracted from zooids of F. sultana cultivated under controlled laboratory conditions. cDNA libraries were prepared and were analyzed by the Illumina paired-ends sequencing. The sequencing data were used for de novo transcriptome assembly and functional annotation. Approximately 118 million clean reads were obtained, and assembled into 85,544 contigs with an average length of 852 bp, an N50 of 1,085 bp, and an average GC content 51.4%. A total of 23,978 (28%) contigs were annotated using BLASTX analysis. Of these transcripts, 4,400 contigs had highest similarity to brachiopod species Lingula anatina. Based on Gene ontology (GO) annotation, the most highly scored categories of biological process were categorized into cellular process (27%), metabolic process (24%), and biological regulation (8%) in the transcriptome of F. sultana. This study gives first insights into the transcriptome of F. sultana and provides comprehensive genetic resources for the species. We believe that the transcriptome of F. sultana will serve as a useful genomic dataset to accelerate research of functional genomics and will help facilitate whole genome sequencing and annotation. Candidate genes potentially involved in growth, proteolysis, and stress/immunity-response were identified, and are worthy of further investigation.

scholarly journals Preliminary Identification of Candidate Genes Related to Survival of Gynogenetic Rainbow Trout (Oncorhynchus mykiss) Based on Comparative Transcriptome Analysis

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1326
Author(s):  
Konrad Ocalewicz ◽  
Artur Gurgul ◽  
Marcin Polonis ◽  
Stefan Dobosz
Keyword(s):  
Rainbow Trout ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Ribosome Biogenesis ◽  
Rna Binding ◽  
Acyl Carrier Protein ◽  
Doubled Haploids ◽  
Regulatory Protein ◽  
Potential Candidate ◽  
Rainbow Trout Oncorhynchus Mykiss

In the present research, the eggs from four rainbow trout females were used to provide four groups of gynogenetic doubled haploids (DHs). The quality of the eggs from different clutches was comparable, however, interclutch differences were observed in the gynogenetic variants of the experiment and the survival of DH specimens from different groups varied from 3% to 57% during embryogenesis. Transcriptome analysis of the eggs from different females exhibited inter-individual differences in the maternal genes’ expression. Eggs originating from females whose gynogenetic offspring had the highest survival showed an increased expression of 46 genes when compared to the eggs from three other females. Eggs with the highest survival of gynogenetic embryos showed an up-regulation of genes that are associated with cell survival, migration and differentiation (tyrosine-protein kinase receptor TYRO3-like gene), triglyceride metabolism (carnitine O-palmitoyltransferase 1 gene), biosynthesis of polyunsaturated fat (3-oxoacyl-acyl-carrier-protein reductase gene), early embryogenic development (protein argonaute-3 gene, leucine-rich repeat-containing protein 3-like gene), 5S RNA binding (ribosome biogenesis regulatory protein homolog) as well as senescence and aging (telomerase reverse transcriptase, TERT gene), among others. Positive correlation between the genotypic efficiency and egg transcriptome profiles indicated that at least some of the differentially expressed genes should be considered as potential candidate genes for the efficiency of gynogenesis in rainbow trout.

Transcriptional profiling of wheat and wheat-rye addition lines to identify candidate genes for aluminum tolerance

2018 ◽  
Vol 62 (4) ◽  
pp. 741-749 ◽  
Author(s):  
N. Salvador-Moreno ◽  
P. R. Ryan ◽  
I. Holguín ◽  
E. Delhaize ◽  
C. Benito ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Transcriptional Profiling ◽  
Aluminum Tolerance ◽  
Addition Lines

scholarly journals Transcriptional Profiling and Functional Analysis of N1/N2 Neutrophils Reveal an Immunomodulatory Effect of S100A9-Blockade on the Pro-Inflammatory N1 Subpopulation

2021 ◽  
Vol 12 ◽  
Author(s):  
Andreea C. Mihaila ◽  
Letitia Ciortan ◽  
Razvan D. Macarie ◽  
Mihaela Vadana ◽  
Sergiu Cecoltan ◽  
...  
Keyword(s):  
Inflammatory Diseases ◽  
Transcriptional Profiling ◽  
Innate Immune ◽  
Potential Contribution ◽  
Functional Differences ◽  
Elevated Expression ◽  
Pharmacological Blockade ◽  
Novel Target ◽  
Increased Activity ◽  
Homogenous Population

Neutrophils have been classically viewed as a homogenous population. Recently, neutrophils were phenotypically classified into pro-inflammatory N1 and anti-inflammatory N2 sub-populations, but the functional differences between the two subtypes are not completely understood. We aimed to investigate the phenotypic and functional differences between N1 and N2 neutrophils, and to identify the potential contribution of the S100A9 alarmin in neutrophil polarization. We describe distinct transcriptomic profiles and functional differences between N1 and N2 neutrophils. Compared to N2, the N1 neutrophils exhibited: i) higher levels of ROS and oxidative burst, ii) increased activity of MPO and MMP-9, and iii) enhanced chemotactic response. N1 neutrophils were also characterized by elevated expression of NADPH oxidase subunits, as well as activation of the signaling molecules ERK and the p65 subunit of NF-kB. Moreover, we found that the S100A9 alarmin promotes the chemotactic and enzymatic activity of N1 neutrophils. S100A9 inhibition with a specific small-molecule blocker, reduced CCL2, CCL3 and CCL5 chemokine expression and decreased MPO and MMP-9 activity, by interfering with the NF-kB signaling pathway. Together, these findings reveal that N1 neutrophils are pro-inflammatory effectors of the innate immune response. Pharmacological blockade of S100A9 dampens the function of the pro-inflammatory N1 phenotype, promoting the alarmin as a novel target for therapeutic intervention in inflammatory diseases.

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