Chiloscyllium plagiosum isolate:BGI_BamShark_2017
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PROVIDER: PRJNA478295 | ENA |
REPOSITORIES: ENA
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Project description:To understand the mechanisms of liver regeneration better to promote research examining liver diseases and marine biology, normal and regenerative liver tissues of Chiloscyllium plagiosum were harvested 0?h and 24?h after partial hepatectomy (PH) and used to isolate small RNAs for miRNA sequencing. In total, 91 known miRNAs and 166 putative candidate (PC) miRNAs were identified for the first time in Chiloscyllium plagiosum. Through target prediction and GO analysis, 46 of 91 known miRNAs were screened specially for cellular proliferation and growth. Differential expression levels of three miRNAs (xtr-miR-125b, fru-miR-204, and hsa-miR-142-3p_R-1) related to cellular proliferation and apoptosis were measured in normal and regenerating liver tissues at 0?h, 6?h, 12?h, and 24?h using real-time PCR. The expression of these miRNAs showed a rising trend in regenerative liver tissues at 6?h and 12?h but exhibited a downward trend compared to normal levels at 24?h. Differentially expressed genes were screened in normal and regenerating liver tissues at 24?h by DDRT-PCR, and ten sequences were identified. This study provided information regarding the function of genes related to liver regeneration, deepened the understanding of mechanisms of liver regeneration, and resulted in the addition of a significant number of novel miRNAs sequences to GenBank.
2013-01-01 | S-EPMC3789328 | BioStudies
Project description:Chiloscyllium plagiosum Genome sequencing and assembly
| PRJNA477737 | ENA
Project description:Chiloscyllium, commonly called bamboo shark, can be found inhabiting the waters of the Indo-West Pacific around East Asian countries such as Malaysia, Myanmar, Thailand, Singapore, and Indonesia. The International Union for Conservation of Nature (IUCN) Red List has categorized them as nearly threatened sharks out of their declining population status due to overexploitation. A molecular study was carried out to portray the systematic relationships within Chiloscyllium species using 12S rRNA and cytochrome b gene sequences. Maximum parsimony and Bayesian were used to reconstruct their phylogeny trees. A total of 381?bp sequences' lengths were successfully aligned in the 12S rRNA region, with 41?bp sites being parsimony-informative. In the cytochrome b region, a total of 1120?bp sites were aligned, with 352 parsimony-informative characters. All analyses yield phylogeny trees on which C. indicum has close relationships with C. plagiosum. C. punctatum is sister taxon to both C. indicum and C. plagiosum while C. griseum and C. hasseltii formed their own clade as sister taxa. These Chiloscyllium classifications can be supported by some morphological characters (lateral dermal ridges on the body, coloring patterns, and appearance of hypobranchials and basibranchial plate) that can clearly be used to differentiate each species.
2014-01-01 | S-EPMC4071782 | BioStudies
Project description:microRNA expression profiling of the normal and regenerating liver of Chiloscyllium plagiosum
| PRJNA293794 | ENA
Project description:Sharks have maintained a key role in marine food webs for 400 million years and across varying physicochemical contexts, suggesting plasticity to environmental change. In this study, we investigated the biochemical effects of ocean acidification (OA) levels predicted for 2100 (pCO2 ~ 900 μatm) on newly hatched tropical whitespotted bamboo sharks (Chiloscyllium plagiosum). Specifically, we measured lipid, protein, and DNA damage levels, as well as changes in the activity of antioxidant enzymes and non-enzymatic ROS scavengers in juvenile sharks exposed to elevated CO2 for 50 days following hatching. Moreover, we also assessed the secondary oxidative stress response, i.e., heat shock response and ubiquitin levels. Newly hatched sharks appear to cope with OA-related stress through a range of tissue-specific biochemical strategies, specifically through the action of antioxidant enzymatic compounds. Our findings suggest that ROS-scavenging molecules, rather than complex enzymatic proteins, provide an effective defense mechanism in dealing with OA-elicited ROS formation. We argue that sharks' ancient antioxidant system, strongly based on non-enzymatic antioxidants (e.g., urea), may provide them with resilience towards OA, potentially beyond the tolerance of more recently evolved species, i.e., teleosts. Nevertheless, previous research has provided evidence of detrimental effects of OA (interacting with other climate-related stressors) on some aspects of shark biology. Moreover, given that long-term acclimation and adaptive potential to rapid environmental changes are yet experimentally unaccounted for, future research is warranted to accurately predict shark physiological performance under future ocean conditions.
2018-01-01 | S-EPMC6111099 | BioStudies
Project description:circRNA-sequencing of Chiloscyllium plagiosum liver
| PRJNA660343 | ENA
Project description:Bacillus amyloliquefaciens-9 (GBacillus-9), which is isolated from the intestinal tract of the white-spotted bamboo shark (Chiloscyllium plagiosum), can secrete potential antibacterial materials, such as ?-1,3-1,4-glucanase and some antimicrobial peptides. However, the low fermentation production has hindered the development of GBacillus-9 as biological additives. In this study, the Plackett-Burman design and response surface methodology were used to optimize the fermentation conditions in a shake flask to obtain a higher yield and antibacterial activity of GBacillus-9. On the basis of the data from medium screening, M9 medium was selected as the basic medium for fermentation. The data from the single-factor experiment showed that sucrose had the highest antibacterial activity among the 10 carbon sources. The Plackett-Burman design identified sucrose, NH4Cl, and MgSO4 as the major variables altering antibacterial activity. The optimal concentrations of these compounds to enhance antibacterial activity were assessed using the central composite design. Data showed that sucrose, NH4Cl, and MgSO4 had the highest antibacterial activities at concentrations of 64.8, 1.84, and 0.08 g L-1, respectively. The data also showed that the optimal fermentation conditions for the antibacterial material production of GBacillus-9 were as follows: Inoculum volume of 5%, initial pH of 7.0, temperature of 36 °C, rotating speed of 180 rpm, and fermentation time of 10 h. The optimal fermentation medium and conditions achieved to improve the yield of antibacterial materials for GBacillus-9 can enhance the process of developing biological additives derived from GBacillus-9.
2020-01-01 | S-EPMC7073760 | BioStudies
Project description:This study aimed to improve our understanding of the mechanisms of liver regeneration in sharks and to identify the microRNAs that participate in liver regeneration and other liver-related diseases. To this end, normal and regenerating liver tissues from C. plagiosum were harvested 0, 3, 6, 12 and 24 h after partial hepatectomy (PH) and were sequenced using the Illumina/Solexa platform. In total, 309 known microRNAs and 590 novel microRNAs were identified in C. plagiosum. There were 368 microRNAs differentially expressed between the normal and regenerating livers. Using target prediction and GO analysis, most of the differentially expressed microRNAs were assigned to functional categories that may be involved in regulating liver regeneration, such as cell proliferation, differentiation and apoptosis. Additionally, this study adds several novel microRNAs to the database, which will help identify microRNAs in other genetically related species and provides a starting point for future studies aimed at understanding the roles of microRNAs in liver regeneration and other liver diseases. Overall design: Sample 1 is the normal C. plagiosum liver, sample 2, sample 3, sample 4 and sample 5 is the regenerating liver obtained 3, 6, 12 and 24 h after PH, respectively.
2016-08-30 | GSE72339 | GEO
Project description:Development of the ability to capture prey is crucial to predator survival. Trends in food-capture performance over early ontogeny were quantified for leopard sharks Triakis semifasciata and whitespotted bamboosharks Chiloscyllium plagiosum by measuring suction pressure and flow in front of the mouth during feeding. At any size, C. plagiosum produce greater subambient pressure and ingest more rounded water parcels. Maximum subambient pressure scaled with negative allometry in T. semifasciata and was accompanied by an increase in the time to reach maximum gape. Despite a similar trend in buccal expansion timing, maximum pressure in C. plagiosum scaled with isometry and was accompanied by an earlier onset of hyoid depression and a positive allometric increase in buccal reserve volume. Growth was the primary factor responsible for developmental trends in both species, with size-independent behavioural changes contributing little to overall performance variability. Ontogenetic dietary shifts are predicted for both species as a consequence of size-dependent changes in performance. Chiloscyllium plagiosum becomes anatomically and behaviourally canalized towards suction feeding, limiting the effective range of prey capture and possibly necessitating stalking. Triakis semifasciata, by contrast, retains the flexibility to employ both ram and suction and therefore captures more elusive prey with age.
1000-01-01 | S-EPMC3226986 | BioStudies