lncRNA-miRNA-mRNA network in kidney transcriptome of Labeo rohita under hypersaline environment

Abstract The present study describes the kidney transcriptome of Labeo rohita, a freshwater fish, exposed to gradually increased salinity concentrations (2, 4, 6 and 8ppt). A total of 10.25 Gbps data was generated, and a suite of bioinformatics tools, including FEELnc, CPC2 and BLASTn were employed for identification of long non-coding RNAs (lncRNAs) and micro RNAs (miRNAs). Our analysis revealed a total of 170, 118, 99, and 269 differentially expressed lncRNA and 120, 118, 99, and 124 differentially expressed miRNAs in 2, 4, 6 and 8 ppt treatment groups respectively. Two competing endogenous RNA (ceRNA) networks were constructed i.e. A* ceRNA network with up-regulated lncRNAs and mRNAs, down-regulated miRNAs; and B* ceRNA network vice versa. 2ppt group had 131 and 83 lncRNA-miRNA-mRNA pairs in A* and B* networks, respectively. 4ppt group featured 163 pairs in A* network and 191 in B* network, while the 6ppt had 103 and 105 pairs. 8ppt group included 192 and 174 pairs. These networks illuminate the intricate RNA interactions in freshwater fish to varying salinity conditions

Interplay of gene expression and regulators under salinity stress in gill of Labeo rohita

Abstract Background Labeo rohita is the most preferred freshwater carp species in India. The concern of increasing salinity concentration in freshwater bodies due to climate change may greatly impact the aquatic environment. Gills are one of the important osmoregulatory organs and have direct contact with external environment. Hence, the current study is conducted to understand the gill transcriptomic response of L. rohita under hypersalinity environment. Results Comprehensive analysis of differentially expressed long non-coding RNAs (lncRNAs), microRNAs (miRNAs) and mRNAs was performed in gills of L. rohita treated with 2, 4, 6 and 8ppt salinity concentrations. Networks of lncRNA-miRNA-mRNA revealed involvement of 20, 33, 52 and 61 differentially expressed lncRNAs, 11, 13, 26 and 21 differentially expressed miRNAs in 2, 4, 6 and 8ppt groups between control and treatment respectively. These lncRNA-miRNA pairs were regulating 87, 214, 499 and 435 differentially expressed mRNAs (DE mRNAs) in 2, 4, 6 and 8ppt treatments respectively. Functional analysis of these genes showed enrichment in pathways related to ion transportation and osmolyte production to cope with induced osmotic pressure due to high salt concentration. Pathways related to signal transduction (MAPK, FOXO and phosphatidylinositol signaling), and environmental information processing were also upregulated under hypersalinity. Energy metabolism and innate immune response pathways also appear to be regulated. Protein turnover was high at 8ppt as evidenced by enrichment of the proteasome and aminoacyl tRNA synthesis pathways, along with other enriched KEGG terms such as apoptosis, cellular senescence and cell cycle. Conclusion Altogether, the RNA-seq analysis provided valuable insights into competitive endogenous (lncRNA-miRNA-mRNA) regulatory network of L. rohita under salinity stress. L. rohita is adapting to the salinity stress by means of upregulating protein turnover, osmolyte production and removing the damaged cells using apoptotic pathway and regulating the cell growth and hence diverting the essential energy for coping with salinity stress

<em>In vitro</em> primary culturing of cells and explant tissue of <em>Conus cumingii</em> venom duct: Cytotoxicity assessment of their culture supernatant on HEK 293T

1096-1102In present study, we attempted to establish primary culture of cells in suspension and tissue explants from the venom duct of Conus cumingii for ample production of conopeptides.  Venom secretary cells migrated from tissue explant within a day and the primary culture cells were successfully maintained up to 20 days. Further, the culture supernatant from both the cell suspension and explant was treated with HEK 293T cells for determining its cytotoxic effects which revealed significant reduction of cell viability giving a prompt evidence for the successful conopetides production by the primary culture in the growth medium

Characterization of Canine Retina Using High-Throughput Sequencing

We performed transcriptome sequencing of canine retinal tissue by 454 GS-FLX and Ion Torrent PGM platforms. RNA-Seq analysis by CLC Genomics Workbench mapped expression of 10,360 genes. Gene ontology analysis of retinal transcriptome revealed abundance of transcripts known to be involved in vision associated processes. The de novo assembly of the sequences using CAP3 generated 29,683 contigs with mean length of 560.9 and N50 of 619 bases. Further analysis of contigs predicted 3,827 fulllength cDNAs and 29,481 (99%) open reading frames (ORFs). In addition, 3,782 contigs were assigned to 316 KEGG pathways which included melanogenesis, phototransduction, and retinol metabolism with 33, 15, and 11 contigs, respectively. Among the identified microsatellites, dinucleotide repeats were 68.84%, followed by trinucleotides, tetranucleotides, pentanucleotides, and hexanucleotides in proportions of 25.76, 9.40, 2.52, and 0.96%, respectively. This study will serve as a valuable resource for understanding the biology and function of canine retina